Category Archives: Water microbiome

April 18, 2017

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Today’s digest hosts a number of rhizosphere-related publications as well as a good amount of interesting microbiome-host-health science.  Coming up next week is BioData World West 2017, a conference focused on Genomics/Precision Medicine/AI that I will be attending – I’ll keep an eye out for anything microbiome-related!

Events and jobs

2017 Metagenomics Workshop – Edwards Lab Event (Bioinformatics)

BioData World West 2017 – Precision Medicine, AI, Genomics Conference

General microbiome

Biological Determinants of Health: Genes, Microbes, and Metabolism Exemplars of Nursing Science – Erin P. Ferranti – Nursing Outlook

* Microbiotal-Host Interactions and Hypertension – Sarah Galla – Physiology

Multi-site human microbiome

* The Landscape Ecology and Microbiota of the Human Nose, Mouth, and Throat – Diana M. Proctor – Cell Host & Microbe

Human respiratory microbiome

* The microbiome in respiratory medicine: current challenges and future perspectives – Rosa Faner – European Respiratory Journal

Human skin microbiome

Living in Peace: Host-Microbiota Mutualism in the Skin – Daniel J. Campbell – Cell Host & Microbe

Human gut microbiome

The Gut Microbiome: Connecting Spatial Organization to Function – Carolina Tropini – Cell Host & Microbe

Lactobacillus casei DG and its postbiotic reduce the inflammatory mucosal response: an ex-vivo organ culture model of post-infectious irritable bowel syndrome – Compare D – BMC Gastroenterology

Animal experiments

Age-Associated Microbial Dysbiosis Promotes Intestinal Permeability, Systemic Inflammation, and Macrophage Dysfunction – Netusha Thevaranjan – Cell Host & Microbe

Animal microbiome

PrePrint – Succession of embryonic and intestinal bacterial communities of Atlantic salmon – Jep Lokesh – bioRxiv

The Role of Rumen Microbiome on Feed Efficiency of Grazing Cattle [page 138] – Leluo Guan – 28th Annual Florida Ruminant Nutrition Symposium

Structure and dynamics of the gut bacterial microbiota of the bark beetle, Dendroctonus rhizophagus (Curculionidae: Scolytinae) across their life stages – Carlos Iván Briones-Roblero – PLOS One

Plant, root, and soil microbiome

The role of soil chemistry and plant neighbourhoods in structuring fungal communities in three Panamanian rainforests – Tyler Schappe – Journal of Ecology

Host plant compatibility shapes the proteogenome of Frankia coriariae – Amir Ktari – Frontiers in Microbiology

Managing and manipulating the rhizosphere microbiome for plant health: A systems approach – Matthew D. Wallenstein – Rhizosphere

In vitro and In vivo biofilm formation by Azotobacter isolates and its relevance to rhizosphere colonization – Mohd. Musheer Altaf – Rhizosphere

Metabolism of pyrene through phthalic acid pathway by enriched bacterial consortium composed of Pseudomonas, Burkholderia, and Rhodococcus (PBR) – Sagar Vaidya – 3 Biotech

Effects of titanium dioxide nanoparticles on soil microbial communities and wheat biomass – Janine Moll – Soil Biology and Biochemistry

The effect of simulated warming on root dynamics and soil microbial community in an alpine meadow of the Qinghai-Tibet Plateau – Changting Wang – Applied Soil Ecology

Water and extremophile microbiome

Impacts of sea-level rise on sediment microbial community structure and function in two New England salt marshes, USA – Matt R. Simon – Journals of Soils and Sediments

A critical assessment of the microorganisms proposed to be important to enhanced biological phosphorus removal in full-scale wastewater treatment systems – Mikkel Stokholm-Bjerregaard – Frontiers in Microbiology

Applicability of cryoconite consortia of microorganisms and glacier-dwelling animals in astrobiological studies – Krzysztof Zawierucha – Contemporary Trends in Geoscience

Built environment

Review – Microbiological diagnosis of device-related biofilm infections – Yijuan Xu – APMIS

Patent Application – MONITORING AND MANAGING A FACILITY MICROBIOME – Dillon, Harrison – Free Patents Online

Microbes in space

Origins of Life on Mars: NASA’s Rovers Were Never Sterilized – Rhawn Gabriel Joseph – Cosmology.com

Phages and viruses

Mini Review Article – Phages in the Human Body – Ferran Navarro – Frontiers in Microbiology

Bioinformatics

* A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes – Wontack Han – Research in Computational Molecular Biology. RECOMB 2017.

Techniques

Effect of environmental variation on estimating the bacterial species richness – Jongjian Chen – Frontiers in Microbiology

Thesis – USE OF MOLECULAR METHODS IN BIOTHREAT PREPAREDNESS – Katja Koskela – National Defense University: Research Publications No. 13

Microbes in the news

Pets During Pregnancy Trigger Gut Bacteria Changes for Infants That May Cut Obesity Risk, Study Finds

Gut microbiome dysregulation implicated in OCD

Microbes on the market

Innovative Microbiome-based IBD Therapeutics to Be Developed Under New Partnership

Microbiome drug candidate prevents recurrence of C. difficile infection

Ed’s non-microbiology picks

Climate change causes glacial river in Yukon to change direction

Self-taught artificial intelligence beats doctors at predicting heart attacks

Stroke rates appear to be rising steadily in young adults

Costs of Selective Attention: When Children Notice What Adults Miss – Daniel J. Plebanek – APS

California Dryness and Recovery Challenge Multi-Century Odds

April 14, 2017

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Quite a number of biofilms based reviews for today’s digest. Local adaptation in natural microbial communities. Bacterial community varies along the natural water balance gradient in the Tibetan Plateau.

Events and jobs

Senior Program Officer  – The Paul G. Allen Frontiers Group – Seattle, WA, United States

 

General microbiome

Culturomics: A New Kid on the Block of OMICS to Enable Personalized Medicine – ME Kambouris – Omics

Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution – T Giraud – Molecular Ecology

*Review: Central venous catheters and biofilms: where do we stand in 2017? – M Gominet – APMIS

 

Human oral microbiome

*Review: Dental biofilm infections – an update – T Larsen – APMIS

*Review: Microbiological diagnosis of device-related biofilm infections – Y Xu – APMIS

*Review: Biofilms in orthopedic infections: a review of laboratory methods – AC Dibartola – APMIS

 

Human vaginal microbiome

Vaginal lactic acid elicits an anti-inflammatory response from human cervicovaginal epithelial cells and inhibits production of pro-inflammatory mediators associated with HIV acquisition – AC Hearps – Mucosal Immunology

*Review: Chronic urinary tract infections in patients with spinal cord lesions – biofilm infection with need for long-term antibiotic treatment – N Tofte – APMIS

 

Human gut microbiome

Curcuminoid Demethylation as an Alternative Metabolism by Human Intestinal Microbiota – S Burapan – Journal of Agricultural and Food Chemistry

Inflammasomes and intestinal inflammation – N Zmora – Mucosal Immunology

Gut Microbial Diversity in Antibiotic-Naive Children After Systemic Antibiotic Exposure: A Randomized Controlled Trial – T Doan – Clinical Infectious Diseases

 

Animal microbiome

Fish oil, lard and soybean oil differentially shape gut microbiota of middle-aged rats – He Li – Scientific Reports

Co-diversification of gastrointestinal microbiota and phylogeny in passerines is not explained by ecological divergence – L Kropáčková – Molecular Ecology

 

Plant, root and soil microbiome

Responses of denitrifying bacterial communities to short-term waterlogging of soils – Y Wang – Scientific Reports

Distinct Soil Microbial Communities in habitats of differing soil water balance on the Tibetan Plateau – Y Li – Scientific Reports

Convergence and contrast in the community structure of Bacteria, Fungi and Archaea along a tropical elevation-climate gradient – KG Peay – FEMS Microbiology Ecology

Continuous production of indole-3-acetic acid by immobilized cells of Arthrobacter agilis – M Ozdal – 3 Biotech

*Review: Agriculturally important microbial biofilms: Present status and future prospects – K Velmourougane – Journal of Basic Microbiology

 

Water and extremophile

Temporal abundance and activity trends of vinyl chloride (VC)-degrading bacteria in a dilute VC plume at Naval Air Station Oceana – Y Liang – Environmental Science and Pollution Research International

Spatial variation in bacterial community in natural wetland-river-sea ecosystems – H Zhang – Journal of Basic Microbiology

Bioremediation Management Reduces Mass Discharge at a Chlorinated DNAPL Site – BR Baldwin – Groundwater Monitoring & Remediation

 

Techniques

Enhancing Multiplex Genome Editing by Natural Transformation (MuGENT) via inactivation of ssDNA exonucleases – TN Dalia – bioRxiv

An Efficient Moments-Based Inference Method for Within-Host Bacterial Infection Dynamics – D Price – bioRxiv

 

More microbes

Dominant bacterial phyla in caves and their predicted functional roles in C and N cycle – S Mandal De – BMC Microbiology

Microbiome yarns: microbiomology of winter rosy face – K Timmis – Microbial Biotechnology

*Review: In vitro studies evaluating the effects of biofilms on wound-healing cells: a review – KR Kirker – APMIS

Vector competence and innate immune responses to dengue virus infection in selected laboratory and field-collected Stegomyia aegypti (= Aedes aegypti) – IM Serrato – Medical and Veterinary Entomology

*Review: Antibiotic treatment of biofilm infections – O Ciofu – APMIS

Microenvironmental characteristics and physiology of biofilms in chronic infections of CF patients are strongly affected by the host immune response – PØ. Jensen – APMIS

 

Microbes in news

To see the unseen: ‘Microbiomes’ show explores the common ground between arts, science – M McINALLY – Gazette-Times

Unprotected sex may disrupt the microbiome in vagina – J Hamzelou – New Scientist

Sol-gel-based stainless steel surface reduces fouling and biofilm formation during milk pasteurization – J Cornall- Dairy Reporter

Gut Microbes Contribute to Age-Associated Inflammation in Mice – A Olena – The Scientist

Microbiome Plus+ Gastrointestinal: New Probiotic Supplement Proven to Increase Vitamin D Levels While Lowering Cholesterol – Military News – Miltech

OPINION: How probiotics research is taking us to the next level of understanding – M Cunningham – Food Navigator

New synthetic peptide promotes wound healing – T Sandle – Digital Journal

Air Pollution Might Make Dangerous Bacteria Harder to Kill – V Greenwood – The Atlantic

Researchers studying how to disrupt bacteria to better treat infections – Phys.org

Bacteria with a bias – K Zehr – UNM HSC Newsbeat

Glowing bacteria could help in landmine cleanup efforts – D Quick – New Atlas

Trump budget plan could sink Shore beaches bacteria reports – R Zimmer – Asbury Park Press

How genetically-altered E.coli strain can kill dangerous bone-eating superbug Pseudomonas aeruginosa – B Crouch – The Advertiser

Study on lactic acid bacteria from kimchi sheds light on treatment of atopic dermatitis – The Korea Herald

This strain of probiotic bacteria treats and protects against anxiety, stress and inflammation – St. Joseph’s Healthcare

 

April 13, 2017

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Profiles of ulcerative colitis patients’ microbiota after fecal microbiota transplantation, a bioinformatics software package for rarefaction analysis, an artist who uses sweat and bacteria to create scents and sculptures.

General microbiome

Review: Microbial metabolites in nutrition, healthcare and agriculture – Rajendra Singh – 3 Biotech

Review: Modified Mediterranean Diet for Enrichment of Short Chain Fatty Acids: Potential Adjunctive Therapeutic to Target Immune and Metabolic Dysfunction in Schizophrenia? – Jamie Joseph – Frontiers in Neuroscience

Human respiratory microbiome

The Nasopharyngeal Microbiota of Children with Respiratory Infections in Botswana – Matthew S Kelly – Pediatric Infectious Disease Journal

Human gut microbiome

* Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation – Susana Fuentes – ISME Journal

Intestinal microbiome in children with severe and complicated acute viral gastroenteritis – Shih-Yen Chen – Scientific Reports

Unusual active site location and catalytic apparatus in a glycoside hydrolase family – Jose Munoz-Munoz – PNAS

Animal experiments

Enterococcus faecalis bacteriocin EntV inhibits hyphal morphogenesis, biofilm formation, and virulence of Candida albicans – Carrie E Graham – PNAS

The therapeutic protection of a living and dead Lactobacillus strain against aluminum-induced brain and liver injuries in C57BL/6 mice – Fengwei Tian & Leilei Yu – PLOS One

Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria – Yusuke Nagara – PLOS One

Review: Caspase recruitment domain 9, microbiota, and tryptophan metabolism: dangerous liaisons in inflammatory bowel diseases – Bruno Lamas – Current Opinion in Clinical Nutrition and Metabolic Care

Individual variation of natural D. melanogaster associated bacterial communities – Yun Wang – bioRxiv

Plant, root, and soil microbiome

A new polyketide glycoside from the rhizospheric Clonostachys rogersoniana associated with Panax notoginseng – Tian-Peng Yin – Journal of Asian Natural Products Research

Bacterial carbon use plasticity, phylogenetic diversity and the priming of soil organic matter – Ember M Morrissey – ISME Journal

Population and function analysis of cultivable bacteria associated with spores of arbuscular mycorrhizal fungus Gigaspora margarita – Liangkun Long – 3 Biotech

Water and extremophile microbiome

Exploring the ecological coherence between the spatial and temporal patterns of bacterioplankton in boreal lakes – Juan P. Niño García – Frontiers in Microbiology

Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems – Sean P Jungbluth – PeerJ

Bacterial community composition and dynamics spanning five years in freshwater bog lakes – Alexandra M Linz – bioRxiv

Occurrence of high-diversity metazoan- to microbial-dominated bioconstructions in a shallow Kimmeridgian carbonate ramp (Jabaloyas, Spain) – G San Miguel – Facies

Expression patterns of elemental cycling genes in the Amazon River Plume – Brandon M Satinsky – ISME Journal

Built environment

Comparison of microbial community shifts in two parallel multi-step drinking water treatment processes – Jiajiong Xu – Applied Microbiology and Biotechnology

Probiotics/prebiotics

Engineered probiotic Escherichia coli can eliminate and prevent Pseudomonas aeruginosa gut infection in animal models – In Young Hwang – Nature Communications

Review: Unraveling the Differences between Gram-Positive and Gram-Negative Probiotics in Modulating Protective Immunity to Enteric Infections – Sukumar Kandasamy – Frontiers in Immunology

Bioinformatics

* RTK: efficient rarefaction analysis of large datasets – Paul Saary – Bioinformatics

A geographically-diverse collection of 418 human gut microbiome pathway genome databases – Aria S Hahn – Scientific Data

Metabolomics

Indolepropionic acid and novel lipid metabolites are associated with a lower risk of type 2 diabetes in the Finnish Diabetes Prevention Study – Vanessa D de Mello – Scientific Reports

More microbes

Influences of dissolved oxygen concentration on biocathodic microbial communities in microbial fuel cells – Laura Rago – Bioelectrochemistry

Microbes in the news

Waste-munching bacteria could make nuclear stores safer – Sam Wong – New Scientist

‘Young poo’ makes aged fish live longer – Ewen Callaway – Nature

Microbiology: Gut microbes augment neurodegeneration – Daniel Erny – Nature

* This Artist Turns Sweat and Bacteria Into Art – Annie Tittiger – Wired

Science, publishing, and career

* Why do scientists fabricate and falsify data? A matched-control analysis of papers containing problematic image duplications – Daniele Fanelli – bioRxiv

Amy’s non-microbiology picks

Human knockouts and phenotypic analysis in a cohort with a high rate of consanguinity – Danish Saleheen – Nature

April 12, 2017

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A pretty broad Digest today, with a promising phylogenetic marker for fungal community studies, a new issue of the Journal of Microbiological Methods, and several news pieces, including one about brain stimulating for weight loss.

Jobs

Microbiology Technician – Lonza America Inc

BMS Microbiology – South West England

General microbiology

*A new promising phylogenetic marker to study the diversity of fungal communities: the GLYCOSIDE HYDROLASE 63 gene – L. Pérez-Izquierdo – Molecular Ecology Resources

pH-Controlled Cerium Oxide Nanoparticle Inhibition of Both Gram-Positive and Gram-Negative Bacteria Growth – Ece Alpaslan – Scientific Reports

Human oral microbiome

The probiotics in dentistry: a narrative review – A.M. Pujia – European Review for Medical and Pharmacological Sciences

Human ear microbiome

Microbiomes of the normal middle ear and ears with chronic otitis media – Shujiro B. Minami – Laryngoscope

Human gut microbiome

PrePrint: Household triclosan and triclocarban exposure impacts the adult intestinal microbiome but not the infant intestinal microbiome – Jessica V. Ribado – bioRxiv

Corrigendum: Antibiotic treatment at delivery shapes the initial oral microbiome in neonates – Luisa F. Gomez-Arango – Scientific Reports

Seven versus 10 days antibiotic therapy for culture-proven neonatal sepsis: A randomised controlled trial – Smriti Rohatgi – Journal of Paediatrics and Child Health

Animal experiments

Metabolic adaptation to the aqueous leaf extract of Moringa oleifera Lam.-supplemented diet is related to the modulation of gut microbiota in mice – Xiaoyu Gao – Applied Microbiology and Biotechnology

Bioactive Molecule from Streptomyces sp Mitigates MDR Klebsiella pneumoniae in Zebrafish Infection Model – Lalitha Cheepurupalli – Frontiers in Microbiology

Animal microbiome

Cassava foliage affects the microbial diversity of Chinese indigenous geese caecum using 16S rRNA sequencing – Mao Li – Scientific Reports

Plant, root and soil microbiome

Biological Control of Bacterial Fruit Blotch of Watermelon Pathogen (Acidovorax citrulli) with Rhizosphere Associated Bacteria – Mahesh Adhikari – The Plant Pathology Journal

Book Chapter: Ecological Restoration Techniques for Management of Degraded, Mined-Out Areas and the Role Played by Rhizospheric Microbial Communities – Prashant Pant & Pratibha Pant – Green Technologies and Environmental Sustainability

Abstract: Consistently inconsistent drivers of patterns of microbial diversity and abundance at macroecological scales – Hendershot JN – Ecology

Population densities of indigenous Acidobacteria change in the presence of plant growth promoting rhizobacteria (PGPR) in rhizosphere – Sadaf Kalam – Journal of Basic Microbiology

Water and extremophile microbiome

Abstract: Salinity and macrophyte drive the biogeography of the sedimentary bacterial communities in a brackish water tropical coastal lagoon – P. Behera – Science of the Total Environment

PDF: The Effects of Soil Environmental Factors on the Colonization of Marine Biocontrol Bacteria – Zenghai Bao – Journal of Residuals Science & Technology

Book chapter: New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles – Bhagwan Rekadwad & Juan M. Gonzalez – Microbial Applications Vol.1

Effects of short-term warming and altered precipitation on soil microbial communities in alpine grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Effects of toxic organic flotation reagent (aniline aerofloat) on an A/O submerged membrane bioreactor (sMBR): Microbial community dynamics and performance – Weixiong Lin – Ecotoxicology and Environmental Safety

Environmental degradation results in contrasting changes in the assembly processes of stream bacterial and fungal communities – Heikki Mykrä – Oikos

Microbes in space

Transcriptomic changes in an animal-bacterial symbiosis under modeled microgravity conditions – Giorgio Casaburi – Scientific Reports

Phages and viruses

iTRAQ-based Proteomic Analysis of Porcine Kidney Epithelial PK15 cells Infected with Pseudorabies virus – Songbai Yang – Scientific Reports

Technology

Release of a new issue of the Journal of Microbiological Methods, with various technical articles of potential interest.

Bioinformatics

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism – Garrett W. Birkel – BMC Bioinformatics

IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models – Chao Ye – Scientific Reports

Quantifying uncertainty of taxonomic placement in DNA barcoding and metabarcoding – Panu Somervuo – Methods in Ecology and Evolution

Microbes in the news

DIRTY PINTS One in three pints served in pubs use ‘bad’ bacteria-filled beer because landlords aren’t cleaning the pumps properly – Sara Kamouni – The Sun

Melioidosis: More cases of potentially fatal bacterium from NT dirt emerge – Eleni Rousos – ABC News

*Magnetic brain stimulation causes weight loss – Tim Sandle – Digital Journal

5 Ways to Ruin Wine Before It’s Even Bottled – Laura Burgess – Vine Pair

A public health failure – Otago Daily Times

Study to develop faster detection of antibiotic resistance – Scoop

Microbes on the market

Superbugs receive a dual drug attack – Kate Dearling – The Badger Online

Breast Milk Helps In The Growth Of Microbes Beneficial To Human Colon, Best For Babies Too – Jezreel Smith – The Science Times

April 11, 2017

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In today’s Microbiome Digest the first interesting study comes not from bacteria but from virus domain. Examining the genomes within a sample from a wastewater treatment plant in Austria, Schulz et al. assembled a previously undiscovered giant virus genome with more genes encoding components of the protein translation machinery than in other giant viruses. The second highlighted  study introduces new oleaginous microalga as a new potential source of compounds for biotechnological applications.

Events and jobs

QC Microbiology Analyst – Dublin, Ireland

Assistant Lecturer in Microbiology – Sligo, Ireland

General microbiome

The genetics of human longevity: an intricacy of genes, environment, culture and microbiome – Serena Dato – Mechanisms of Ageing and Development

Pregnancy and early life

Correlation between early-life regulation of the immune system by microbiota and allergy development – Thomas Gensollen – Journal of Allergy and Clinical Immunology

Microbial Community Assembly And Metabolite Profile Of The Gut Microbiome In Extremely Low Birthweight Infants – Stephen Wandro – bioRxiv

Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum – Chihaya Yamada – Cell Chemical Biology

A Comparative Study of Oral Microbiota in Infants with Complete Cleft Lip and Palate or Cleft Soft Palate – Agnieszka Machorowska-Pieniążek – BioMed Research International

Effect of probiotics on digestibility and immunity in infants: A study protocol for a randomized controlled trial – Lingli Xiao – Medicine

Human respiratory microbiome

Airway microbial dysbiosis in asthmatic patients: A target for prevention and treatment? – Kian Fan Chung – Journal of Allergy and Clinical Immunology

Oral microbiome

Measuring nitrate reductase activity from human and rodent tongues – Khandaker Ahtesham Ahmed – Nitric Oxide

Streptococcal adhesin SspA/B analogue peptide inhibits adherence and impacts biofilm formation of Streptococcus mutans – Tatsuro Ito – PLOSOne

Characterization of growth inhibition of oral bacteria by sophorolipid using a microplate-format assay – Daniel K.Y. Solaiman – Journal of Microbiological Methods

Salivary microbiome of an urban Indian cohort and patterns linked to subclinical inflammation  – Aneesha Acharya – Oral Diseases

Second Era of OMICS in Caries Research: Moving Past the Phase of Disillusionment – M.M. Nascimento – Journal of Dental Research

Human skin microbiome

Bacterial communities on facial skin of teenage and elderly Thai females – Naraporn Somboonna – Archives of Microbiology

Skin microbiome and mast cells – Satomi Igawa – Translational Research

Human vaginal microbiome
Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions – John J. Schellenberg – Journal of Microbiological Methods

‘Anaerococcus mediterraneensis’ sp. nov., a new species isolated from human female genital tract – K. Diop – New Microbes and New Infections

Human gut microbiome

Functional relevance of microbiome signatures: The correlation era requires tools for consolidation – Ludovica F. Buttó – Journal of Allergy and Clinical Immunology

Physiochemical Tuning of Potent Escherichia coli Anti-Adhesives by Microencapsulation and Methylene Homologation – Dimitri Alvarez Dorta – ChemMedChem

Gut microbiota functions: metabolism of nutrients and other food components –  Ian Rowland – European Journal of Nutrition

Evaluation of the impact of gut microbiota on uremic solute accumulation by a CE-TOFMS–based metabolomics approach – Eikan Mishima – Kidney International

Animal experiments

Starch-enriched diet modulates the glucidic profile in the rat colonic mucosa – Maria Gabriella Gabrielli – European Journal of Nutrition

The influence of diet on the grass carp intestinal microbiota and bile acids – Jing Zhang – Aquaculture Research

Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves – D.E. Gomez – Journal of Veterinary Internal Medicine

Gut Microbiota Modulation Attenuated the Hypolipidemic Effect of Simvastatin in High-Fat/Cholesterol-Diet Fed Mice – Xuyun He – Journal of Proteome Research

 

Animal microbiome

Host Genotype and Microbiota Contribute Asymmetrically to Transcriptional Variation in the Threespine Stickleback Gut – Clayton M. Small – Genome Biology and Evolution

The structured diversity of specialized gut symbionts of the New World army ants – Piotr Łukasik – Molecular Ecology

Microbial composition of spiny ants (Hymenoptera: Formicidae: Polyrhachis) across their geographic range – Manuela Oliveira Ramalho – BMC Evolutionary Biology

Plant, root, and soil microbiome

Isolation, identification, and environmental adaptability of heavy-metal-resistant bacteria from ramie rhizosphere soil around mine refinery – Jie Jiang – Biotech

Autogenic succession and deterministic recovery following disturbance in soil bacterial communities – Stephanie D. Jurburg – Scientific Reports

Microbial community response to hydration-desiccation cycles in desert soil – Adam Šťovíček – Scientific Reports

Water and extremophile microbiome

Development of an economical, autonomous pHstat system for culturing phytoplankton under steady state or dynamic conditions – Rachel L. Golda – Journal of Microbiological Methods

Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods – Sarita Pudasaini – Frontiers in Microbiology

Subduction zone forearc serpentinites as incubators for deep microbial life – Oliver Plümper – PNAS

Ferrous iron- and ammonium-rich diffuse vents support habitat-specific communities in a shallow hydrothermal field off the Basiluzzo Islet (Aeolian Volcanic Archipelago) – G. Bortoluzzi – Geobiology

Microbial biotechnology

Characterization of a Chlorophyta microalga isolated from a microbial mat in Salar de Atacama (northern Chile) as a potential source of compounds for biotechnological applications – Gladys Hayashida – Phycological Research

Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae – Vineeta Rai – Scientific Reports

Food microbiology

Microbial communities associated with the anthropogenic, highly alkaline environment of a saline soda lime, Poland – Agnieszka Kalwasińska – Antonie van Leeuwenhoek

Probiotics / prebiotics

Genome Sequences of Potential Probiotic Lactobacillus rhamnosus Isolates from Human Infants – Jason W. Arnold – Genome Announcements

Phages and viruses

Review: Phage injection establishes CRISPR immunity – Shimona Starling – Nature Reviews Microbiology

Giant viruses with an expanded complement of translation system components – Frederik Schulz – Science

Bioinformatics

The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism – Garrett W. Birkel – BMC Bioinformatics

Techniques

Identification of microorganisms grown on chromogenic media by MALDI-TOF MS – Petra Lüthje – Journal of Microbiological Methods

The impact of fecal sample processing on prevalence estimates for antibiotic-resistant Escherichia coli – Sylvia Omulo – Journal of Microbiological Methods

Chapter in the book: New Generation DNA Sequencing (NGS): Mining for Genes and the Potential of Extremophiles – Bhagwan Rekadwad – Microbial Applications Vol.1

Novel micelle PCR-based method for accurate, sensitive and quantitative microbiota profiling – Stefan A. Boers – Scientific Reports
Microbes in the news 

Bacteria to the Future – Mizzou News (University of Missouri)

April 8, 2017

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General microbiome

Modeling The Consequences Of Heterogeneity In Microbial Population Dynamics – Helena Herrmann – BioRxiv

Human respiratory microbiome

16S rRNA Gene Sequencing Reveals Site-Specific Signatures Of The Upper And Lower Airways Of Cystic Fibrosis Patients – Sarah K. Lucas – BioRxiv

Review: Airway microbial dysbiosis in asthmatic patients: A target for prevention and treatment? – Kian Fan Chung – The Journal of Allergy and Clinical Immunology

Human skin microbiome

Toxification of polycyclic aromatic hydrocarbons by commensal bacteria from human skin – Juliane Sowada – Archives of Toxicology

Human gut microbiome

Long-term use of antibiotics and risk of colorectal adenoma – Yin Cao – Gut

Changes in Composition of the Gut Bacterial Microbiome after Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in a Pediatric Heart Transplant Patient – Kyle L. Flannigan – Frontiers in Cardiovascular Medicine

Animal experiments

Iron Supplements Modulate Colon Microbiota Composition and Potentiate the Protective Effects of Probiotics in Dextran Sodium Sulfate-induced Colitis – Marco Constante – Inflammatory Bowel Diseases

Animal microbiome

Intestinal microbiota of healthy and unhealthy Atlantic salmon Salmo salar L. in a recirculating aquaculture system – Chun Wang – Chinese Journal of Oceanology and Limnology

Identification and modes of action of endogenous bacteria in taphonomy of embryos and larvae – Justin L. Eagan – Palaios

Microbial community compositions in the gastrointestinal tract of Chinese Mongolian sheep using Illumina MiSeq sequencing revealed high microbial diversity – Yan Zeng – AMB Express

Skin microbiota differs drastically between co-occurring frogs and newts – Molly C. Bletz – The Royal Society Open Science

Amphibian skin microbiota exhibits temporal variation in community structure but stability of predicted Bd-inhibitory function – Molly C Bletz – ISME

Plant, root, and soil microbiome

Characterization of a metagenome-derived protease from contaminated agricultural soil microorganisms and its random mutagenesis – Chengjian Jiang – Folia Microbiologica

Metagenomic analysis exploring taxonomic and functional diversity of soil microbial communities in Chilean vineyards and surrounding native forests – Luis E Castañeda – PeerJ

Initial nitrogen enrichment conditions determines variations in nitrogen substrate utilization by heterotrophic bacterial isolates – Suchismita Ghosh – BMC Microbiology

Sequential bioavailability of sedimentary organic matter to heterotrophic bacteria – Nagissa Mahmoudi – Environmental Microbiology

Seasonal and interannual dynamics of soil microbial biomass and available nitrogen in an alpine meadow in the eastern part of Qinghai-Tibet Plateau, China – Bo Xu – Biogeosciences

Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration – Deepak Kumaresan – Scientific Reports

Keystone microbial taxa regulate the invasion of a fungal pathogen in agro-ecosystems – P. Trivedi – Soil Biology and Biochemistry

Water and extremophile microbiome

Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater – William B. Ludington – PLOS ONE

Hidden diversity revealed by genome-resolved metagenomics of iron-oxidizing microbial mats from Lō’ihi Seamount, Hawai’i – Heather Fullerton – ISME

Performance and microbial community analysis in a modified anaerobic inclining-baffled reactor treating recycled paper mill effluent – Haider M. Zwain – Environmental Science and Pollution Research

Microbial formation of labile organic carbon in Antarctic glacial environments – H. J. Smith – Nature Geoscience

Review: Cryospheric science: The power of glacial microbes – Elizabeth B. Kujawinski – Nature Geoscience

Taxonomic composition of Lake Baikal bacterioneuston communities – A. D. Galach’yants – Microbiology

Performance and microbial population dynamics during stable operation and reactivation after extended idle conditions in an aerobic granular sequencing batch reactor – Qiulai He – Bioresource Technology

Comparative metagenomics reveals insights into the deep-sea adaptation mechanism of the microorganisms in Iheya hydrothermal fields – Hai-liang Wang – Journal of Marine Systems

Built environment

Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City – Julia M. Maritz – PLOS ONE

Food microbiology

The Dynamic Microbiota Profile During Pepper (Piper nigrum L.) Peeling by Solid-State Fermentation – Qisong Hu – Current Microbiology

Molecular investigation of bacterial communities during the manufacturing and ripening of semi-hard Iranian Liqvan cheese – M. Ramezani – Food Microbiology

Identification of microbial communities, with a focus on foodborne pathogens, during kimchi manufacturing process using culture-independent and -dependent analyses – Hae-Won Lee – LWT – Food Science and Technology

Probiotics / prebiotics

Impact of probiotic Saccharomyces boulardii on the gut microbiome composition in HIV-treated patients: A double-blind, randomised, placebo-controlled trial – Judit Villar-García – PLOS ONE

Phages and viruses

Taxonomic variability and functional stability in microbial communities infected by phages – Stilianos Louca – Environmental Microbiology

Bioinformatics

EzMap: A Simple Pipeline for Reproducible Analysis of the Human Virome – Patrick Czeczko – Bioinformatics

Microbes in the news

You Should Appreciate Germs – Bill Gates

Microbes on the market

The expanding ecosystem of microbiome startups – Juliet Preston – MedCity News

April 5, 2017

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Today’s digest features interesting research on the dynamic microbiome evolution in social bees and the alteration in quorum Sensing, cell motility, stress Response, and carbohydrate metabolism  of gut microbiome by the organophosphate pesticide Diazinon. Low dose penicillin in early life can induce long term changes in mice gut microbiota, brain cytokines and behavior. Interesting reviews on the microbiome and human biology, and role of gut microbiota in the development of hypertension, including that associated with obstructive sleep apnea.

General microbiome

*Review: The Microbiome and Human Biology – Rob Knight – Annual Review of Genomics and Human Genetics

*Dynamic microbiome evolution in social bees – Waldan K. Kwong – Science Advances

Anaerobic Bacterial Fermentation Products Increase Tuberculosis Risk in Antiretroviral-Drug-Treated HIV – Leopoldo N. Segal – Cell Host & Microbe

Pregnancy and early life

Vancomycin treatment is a risk factor for vancomycin-nonsusceptible Staphylococcus capitis sepsis in preterm neonates – Marine Butin – Clinical Microbiology and Infection

Human oral microbiome

Relative abundance of total subgingival plaque-specific bacteria in salivary microbiota reflects the overall periodontal condition in patients with periodontitis – Shinya Kageyama – Plos One

Review: Biofilm over teeth and restorations: What do we need to know? – Nancy J. Lin – Dental Materials

Human skin microbiome

Cutaneous Burn Injury Promotes Shifts in the Bacterial Microbiome in Autologous Donor Skin: Implications for Skin Grafting Outcomes – Jennifer K. Plichta – Shock

Human gut microbiome

Review : The gut microbiota: a possible factor influencing systemic lupus erythematosus – Hadar Neuman – Current Opinion in Rheumatology

*Organophosphate Diazinon Altered Quorum Sensing, Cell Motility, Stress Response, and Carbohydrate Metabolism of Gut Microbiome – Bei Gao -Toxicological Sciences

Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab – N. Chaput – Oncology

*Review: Obstructive Sleep Apnea-Induced Hypertension: Role of the Gut Microbiota – David J. Durgan – Current Hypertension Reports

Review: The Gut Microbiota and Alzheimer’s Disease – Chunmei Jiang – Journal of Alzheimer’s Disease

Fecal Microbiota Transplantation

Fecal Microbiota Transplantation in Patients with Blood Disorders Inhibits Gut Colonization with Antibiotic-Resistant Bacteria: Results of a Prospective, Single-Center Study – Jaroslaw Bilinski – Clinical Infectious Diseases

Animal microbiome

Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes – Tongtong Li – Frontiers in Microbiology

Diurnal Dynamics of Gaseous and Dissolved Metabolites and Microbiota Composition in the Bovine Rumen – Henk J. van Lingen – Frontiers in Microbiology

Microbial Biogeography and Core Microbiota of the Rat Digestive Tract – Dongyao Li – Scientific Reports

Animal experiments

Bifidobacterium in the gut microbiota confer resilience to chronic social defeat stress in mice – Chun Yang – Scientific Reports

Lack of Evidence That Selenium-Yeast Improves Chicken Health and Modulates the Caecal Microbiota in the Context of Colonization by Campylobacter jejuni – Alexandre Thibodeau – Frontiers in Microbiology

Review : Outstanding animal studies in allergy II: from atopic barrier and microbiome to allergen-specific immunotherapy – Erika Jensen-Jarolim – Current Opinion in Allergy & Clinical Immunology

Faecalibacterium prausnitzii treatment improves hepatic health and reduces adipose tissue inflammation in high-fat fed mice – Eveliina Munukka – ISME Journal

*Low-dose penicillin in early life induces long-term changes in murine gut microbiota, brain cytokines and behavior –  Sophie Leclercq – Nature Communications

Nod2 and Nod2-regulated microbiota protect BALB/c mice from diet-induced obesity and metabolic dysfunction – Ivan Rodriguez-Nunez – Scientific Reports

Plant, root, and soil microbiome

Aluminum-tolerant bacteria improve the plant growth and phosphorus content in ryegrass grown in a volcanic soil amended with cattle dung manure – María de la Luz Mora- Applied Soil Ecology

Invisible but consequential: root endophytic fungi have variable effects on belowground plant–insect interactions – Huyijuie Gan – Ecosphere

Land-use types and soil chemical properties influence soil microbial communities in the semiarid Loess Plateau region in China – Qin Tian – Scientific Reports

Phylogenetic conservation of substrate use specialization in leaf litter bacteria – Kristin L. Dolan – Plos ONE

Root biomass and exudates link plant diversity with soil bacterial and fungal biomass – Nico Eisenhauer – Scientific Reports

Water and extremophile microbiome

Discrimination of Four Marine Biofilm-Forming Bacteria by LC-MS Metabolomics and Influence of Culture Parameters – Laurie Favre – Journal of Proteome Research

Iron assimilation and utilization in anaerobic ammonium oxidizing bacteria – Christina Ferousi – Current Opinion in Chemical Biology

*Potential sources of bacteria colonizing the cryoconite of an Alpine glacier – Andrea Franzetti – PLOS ONE

Spatio-Temporal Variations of Marine Biofilm Communities Colonizing Artificial Substrata Including Antifouling Coatings in Contrasted French Coastal Environments – Jean-François Briand – Microbial Ecology

Metabolomics

Review: Metabolomics: Strategies to Define the Role of Metabolism in Virus Infection and Pathogenesis – Marianne Manchester – Advances in Virus Research

Effect of Major Royal Jelly Proteins on Spatial Memory in Aged Rats: Metabolomics Analysis in Urine – Di Chen -Journal of Agricultural and Food Chemistry

Food microbiology

Sourdough authentication: quantitative PCR to detect the lactic acid bacterial microbiota in breads – Erica Pontonio – Scientific Reports

Probiotics / prebiotics

Evaluation of Potential Probiotics Isolated from Human Milk and Colostrum – Quésia S. Damaceno – Probiotics and Antimicrobial Proteins

Bioinformatics

SLIMM: species level identification of microorganisms from metagenomes – Temesgen Hailemariam Dadi – PeerJ

Techniques

Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area – Kazuma Nakano – Human Cell

High-pressure microscopy for tracking dynamic properties of molecular machines – Masayoshi Nishiyama – Biophysical Chemistry

Gut Microbiome Standardization in Control and Experimental Mice – Kathy D. McCoy – Current Protocols in Immunology

Diastereomer-specific Quantification of Bioactive Hexosylceramides from Bacteria and Mammals – Johanna von Gerichten – Journal of Lipid Research

Microbes in the news

Genetically engineered microbes make their own fertilizer, could feed the world’s poorest

The Next Plague (5) Bacteria: The Coming And Going And Coming Again Of Bacterial Plagues

Latest Helicobacter pylori breakthrough could lead to eradication of bacteria

Science, publishing, and career

Journal editor calls for ‘culture change’ around clinical trial data

Anitha’s non-microbiology picks

In the quest of Planet 9

April 4, 2017

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General microbiome

Diversity of fungus-growing termites (Macrotermes) and their fungal symbionts (Termitomyces) in the semiarid Tsavo Ecosystem, Kenya – R Vesala – Biotropica

Indole signalling and (micro)algal auxins decrease the virulence of Vibrio campbellii, a major pathogen of aquatic organisms – Q Yang – Environmental Microbiology

Large population study shows that adolescents with celiac disease have an increased risk of multiple autoimmune and nonautoimmune comorbidities –  A Assa – Acta Paediatrica

In vitro fermentation of oat β-glucan and hydrolysates by fecal microbiota and selected probiotic strains – JL Dong – Journal of the Science of Food and Agriculture

 

Human gut microbiome

Gastric microbiota features associated with cancer risk factors and clinical outcomes: A pilot study in gastric cardia cancer patients from Shanxi, China – G Yu – International Journal of Cancer

 

Animal microbiome

Host species shapes the co-occurrence patterns rather than diversity of stomach bacterial communities in pikas – H Li – Applied Microbiology and Biotechnology

 

Plant, root and soil microbiome

Phylloplane bacteria increase the negative impact of food limitation on insect fitness – GL Olson – Ecological Entomology

Bodyguards: Pathogen-Derived Decoys That Protect Virulence Factors – JK Paulus – Trends in Plant Science

Response of the rhizosphere prokaryotic community of barley (Hordeum vulgare L.) to elevated atmospheric CO2 concentration in open-top chambers – M Szoboszlay – Microbiology Open

Draft Genome Sequence of Pseudomonas putida Strain GM4FR, an Endophytic Bacterium Isolated from Festuca rubra L. – F Wemheuer – Genome Announcements

Phytoremediation of Petroleum-Contaminated Soil in Association with Soil Bacteria – P Pokethitiyook – Phytoremediation

Phytoremediation of Salt-Impacted Soils and Use of Plant Growth-Promoting Rhizobacteria (PGPR) to Enhance Phytoremediation – KE Gerhardt – Phytoremediation

Genomic identification and characterization of the elite strains Bradyrhizobium yuanmingense BR 3267 and Bradyrhizobium pachyrhizi BR 3262 recommended for cowpea inoculation in Brazil – J Leite – Brazilian Journal of Microbiology

Effect of elevated nitrate on biodegradation of pentabromodiphenyl ether (BDE-99) and change in microbial communities during groundwater recharge with tertiary-treated municipal wastewater – Y Yan – International Biodeterioration & Biodegradation

The tale of a neglected energy source: Elevated hydrogen exposure affects both microbial diversity and function in soil – M Khdhiri – Applied and Environmental Microbiology

 

Water and extremophile microbiome

Production and persistence of bacterial and labile organic matter at the hypoxic water–sediment interface of the St. Lawrence Estuary – M Hébert – Limnology and Oceanography

Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria – S Muthusamy – Environmental Microbiology

Spatiotemporal dynamics of bacterial community composition in large shallow eutrophic Lake Taihu: High overlap between free-living and particle-attached assemblages – X Tang – Limnology and Oceanography

 

Built environment

Coarse-graining bacteria colonies for modelling critical solute distributions in picolitre bioreactors for bacterial studies on single-cell level – C Westerwalbesloh – Microbial Biotechnology

 

Phages and Virus

Short-Sighted Virus Evolution and a Germline Hypothesis for Chronic Viral Infections – KA Lythgoe – Trends in Microbiology

Conflicting selection alters the trajectory of molecular evolution in a tripartite bacteria–plasmid–phage interaction – E Harrison – Molecular Ecology

 

Techniques

*Review: Bioelectrochemical Systems for Measuring Microbial Cellular Functions – HMM Selim – Electroanalysis

Engineering bacterial thiosulfate and tetrathionate sensors for detecting gut inflammation – KNM Daeffler – Molecular Systems Biology

Impact of Contaminating DNA in Whole Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis – M Thoendel – Journal of Clinical Microbiology

Genomics and Metagenomics in Microbial Ecology: Recent Advances and Challenges  – T Narihiro – Microbes and Environments

A metagenomic approach to decipher the indigenous microbial communities of arsenic contaminated groundwater of Assam –  S Das – Genomics Data

Optimization of a bioassay to evaluate Escherichia coli stress responses – B Cunha – IEEE

 

More microbes

*Review: Shapeshifting to Survive: Shape Determination and Regulation in Caulobacter crescentus – SA Woldemeskel – Trends in Microbiology

 

Microbes in news

Antibiotic Resistant Bacteria Common in Diabetic Foot Ulcers – S Gupta – Endocrinology Advisor

Fighting Antibiotic-Resistant Bacteria in Food Animals – J Bartel – Veterinary Medicine News

Vets warn dog owners about potentially deadly bacteria lurking in water – A Lasker – Lifestyle

Magnetic brain stimulation causes weight loss by making gut bacteria healthier – The Endocrine Society – Science Daily

Vapour droplets from threatened orcas show pneumonia bacteria – Waterloo Region Record – TheRecord.com

Hitchhiking Earth bacteria could evolve to live on Mars – M Irving – New Atlas

Bionic leaf turns air, water, sunlight and bacteria into fertilizer – B Hays – UPI

Nicholls sophomore researches antibiotic-resistant bacteria – G Ohlmeyer – Houmatoday.com

What the Bacteria in Your Mouth May Reveal About Your Cancer Risk – SG Miller – Live Science

April 1, 2017

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Events and jobs

Asst/Assoc Collegiate-Track Clinical Microbiology Faculty – Virginia Tech

General microbiome

Salivary inflammatory markers and microbiome in normoglycemic lean and obese children compared to obese children with type 2 diabetes – Waleed F. Janem – PLOS ONE

Microbiome study finds children with type 2 diabetes more likely to have poor oral health – Ellen Goldbaum – Medical Xpress

Cross-talk among metabolic parameters, esophageal microbiota, and host gene expression following chronic exposure to an obesogenic diet – Nadeem O. Kaakoush – Scientific Reports

Review: Microbiome Tools for Forensic Science – Jessica L. Metcalf – Trends in Biotechnology

Book: Forensic Microbiology – David O. Carter

Review: The legacy of the past: effects of historical processes on microbial metacommunities – Máté Vass – Aquatic Microbial Ecology

Human respiratory microbiome

The microbiome and secondary lung disease in neuromuscular patients: Is it time to change our clinical practice? – Reply – Florian Stehling – Respirology

Human skin microbiome

Patterns in the skin microbiota differ in children and teenagers between rural and urban environments – Jenni Lehtimäki – Scientific Reports

Human vaginal microbiome

Transient microbiota exposures activate dormant Escherichia coli infection in the bladder and drive severe outcomes of recurrent disease – Nicole M. Gilbert – PLOS Pathogens

Vaginal bacteria can trigger recurrent UTIs, study shows – Science Daily

Human gut microbiome

Review: Diet and microbiota in inflammatory bowel disease: The gut in disharmony – Davy CM Rapozo – World Journal of Gastroenterology

The microbiome of professional athletes differs from that of more sedentary subjects in composition and particularly at the functional metabolic level – Wiley Barton – Gut

Animal experiments

NLRP12 regulates gut microbiota to suppress intestinal inflammation – Katrina Ray – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Community structure of the gut microbiota in sympatric species of wild Drosophila – Vincent G. Martinson – Ecology Letters

Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq – Alexandra Grote – PLOS Neglected Tropical Diseases

Researchers profile symbiotic relationship between bacteria and filarial nematodes – Medical Xpress

The Bacterial Community Found on the surface Purple Martin (Progne subis) Eggs – Beth A. Potter – The Open Ornithology Journal

Stable mucus-associated bacterial communities in bleached and healthy corals of Porites lobata from the Arabian Seas – Ghaida Hadaidi – Scientific Reports

Plant, root, and soil microbiome

Relationship of microbial communities and suppressiveness of Trichoderma fortified composts for pepper seedlings infected by Phytophthora nicotianae – Margarita Ros – PLOS ONE

Two-year field monitoring shows little evidence that transgenic potato containing ABF3 significantly alters its rhizosphere microbial community structure – Ki Jung Nam – Journal of Ecology and Environment

Members of Gammaproteobacteria as indicator species of healthy banana plants on Fusarium wilt-infested fields in Central America – Martina Köberl – Scientific Reports

Review: From yogurt to yield: Potential applications of lactic acid bacteria in plant production – John R. Lamont – Soil Biology and Biochemistry

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses – Tianzhu Li – PLOS ONE

Water and extremophile microbiome

Impact of selectively enriched microbial communities on long-term fermentative hydrogen production – R.K. Goud – Bioresource Technology

Co-invasion hypothesis explains microbial community structure changes in upland streams affected by riparian invader – Paul J. McInerney – Freshwater Science

Silver nanoparticles uptake by salt marsh plants – Implications for phytoremediation processes and effects in microbial community dynamics – Joana P. Fernandes – Marine Pollution Bulletin

Food microbiology

Identification of Microbial Profile of Koji Using Single Molecule, Real-Time Sequencing Technology – Wenyan Hui – Journal of Food Science

Probiotics / prebiotics

Roles of Probiotic Lactobacilli Inclusion in Helping Piglets Establish Healthy Intestinal Inter-environment for Pathogen Defense – Jiajun Yang – Probiotics and Antimicrobial Proteins

Phages and viruses

Review: Intriguing interaction of bacteriophage-host association: An understanding in the era of omics – Krupa M. Parmar – Frontiers in Microbiology

Bioinformatics

Review: Are Next-Generation Sequencing Tools Ready for the Cloud? – Antonio Celesti – Trends in Biotechnology

Techniques

Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP) – Scott Tighe – Journal of Biomolecular Technology

In vitro gene expression-coupled bacterial cell chip for screening species-specific antimicrobial enzymes – Seok-Joon Kwon – Journal of Biotechnology and Bioengineering

Review: International Standards for Genomes, Transcriptomes, and Metagenomes – Christopher E. Mason – Journal of Biomolecular Technology

A comparison of sampling methods for examining the laryngeal microbiome – Alissa S. Hanshew – PLOS ONE

Microbes in the news

Probiotics For Babies: Why Your Baby’s Gut Health Is So Important –  Joy D’Souza – The Huffington Post Canada

NIH Wants to Test New Bacteria Therapy for Eczema – Maggie Fox – NBC News

Microbes on the market

Regulator OKs bacteria’s spread – Martin Cash – Winnipeg Free Press

March 30, 2017

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Midgut microbiome of a vector for leishmaniasis, reviews on the human oral microbiome, using microfluidics to visualize live root-bacteria interactions, new open-access publishing project from the Gates Foundation.

General microbiome

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions – Babak Moment – eLIFE

Human oral microbiome

Review: Oral Microbiome and Nitric Oxide: the Missing Link in the Management of Blood Pressure – Nathan S. Bryan – Current Hypertension Reports

Review: Microbiota, Immune Subversion, and Chronic Inflammation – Carolyn D Kramer – Frontiers in Microbiology

Human gut microbiome

Highlight: Shaping the gut microbiome from the pancreas – Wei Wong – Science Signaling

Review: Mechanisms and consequences of intestinal dysbiosis – G. Adrienne Weiss – Cellular and Molecular Life Sciences

Animal experiments

Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse – Alessandro Tanca – Frontiers in Microbiology

Helminth-induced alterations of the gut microbiota exacerbate bacterial colitis – C Su – Mucosal Immunology

Sex-related alterations of gut microbiota composition in the BTBR mouse model of autism spectrum disorder – Lorena Coretti – Scientific Reports

Milk Fat Globule Membrane Supplementation in Formula Modulates the Neonatal Gut Microbiome and Normalizes Intestinal Development – Ganive Bhinder – Scientific Reports

Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency – Wei Yan – Scientific Reports

Animal microbiome

An integrated overview of the midgut bacterial flora composition of Phlebotomus perniciosus, a vector of zoonotic visceral leishmaniasis in the Western Mediterranean Basin – Wael Fraihi – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

* Live imaging of root–bacteria interactions in a microfluidics setup – Hassan Massalha – PNAS

Mechanisms of nitrogen deposition effects on temperate forest lichens and trees – Therese S. Carter – Ecosphere

Research priorities for harnessing plant microbiomes in sustainable agriculture – Posy E Busby – PLOS Biology

Fe plaque-related aquatic uranium retention via rhizofiltration along a redox-state gradient in a natural Phragmites australis Trin ex Steud. wetland – Weqing Wang – Environmental Science and Pollution Research

Functional and phylogenetic diversity of cultivable rhizobacterial endophytes of sorghum [Sorghum bicolor (L.) Moench] – Venkadasamy Govindasamy – Antonie van Leeuwenhoek

Enhanced growth of halophyte plants in biochar-amended coastal soil: roles of nutrient availability and rhizosphere microbial modulation – Hao Zheng – Plant, Cell & Environment

Water and extremophile microbiome

Metagenomic Analysis of a Complex Community Present in Pond Sediment – Vivek Negi – Journal of Genomics

Probiotics/prebiotics

The preliminary study of prebiotic potential of Polish wild mushroom polysaccharides: the stimulation effect on Lactobacillus strains growth – Renata Nowak – European Journal of Nutrition

Probiotics may delay the progression of nonalcoholic fatty liver disease by restoring the gut microbiota structure and improving intestinal endotoxemia – Li Xue – Scientific Reports

Bioinformatics

MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool – Bin Zou – PLOS One

Metabolomics

Gas chromatography/mass spectrometry metabolomics of urine and serum from nonhuman primates exposed to ionizing radiation: Impacts on the tricarboxylic acid cycle and protein metabolism – Evan L Pannkuk – Journal of Proteome Research

Techniques

Review: Pretreatment methods of lignocellulosic biomass for anaerobic digestion – Farrukh Raza Amin – AMB Express

Comparison of Standard Culture-Based Method to Culture-Independent Method for Evaluation of Hygiene Effects on the Hand Microbiome – C Zapka – mBio

More microbes

Depleting Mycobacterium tuberculosis of the transcription termination factor Rho causes pervasive transcription and rapid death – Laure Botella – Nature Communications

A Pseudomonas T6SS effector recruits PQS-containing outer membrane vesicles for iron acquisition – Jinshui Lin – Nature Communications

Indole-Induced Activities of β-Lactamase and Efflux Pump Confer Ampicillin Resistance in Pseudomonas putida KT2440 – Jisun Kim – Frontiers in Microbiology

Microbes in the news

Microbiome: Puppy power – Sujata Gupta – Nature (Outlook section)

Biological underpinnings of chronic fatigue syndrome begin to emerge – Amy Maxmen – Nature (News section)

Bacteria from sewage are infecting coral reefs – Elena Motivans – ZME Science

Key research priorities for agricultural microbiomes identified – Phys Org

Viral Bacterial Parasites Called Phages Drive Co-Evolution of Gut Microbiome – MedicalResearch.com

MSU, Shedd Aquarium partnering to create healthier aquatic homes – EurekAlert

Painting with bacteria is a thing and BUGSS will show you how – Stephen Babcock – Technical.ly Baltimore

Microbes on the market

Marrone Bio Innovations and Evogene Advance Novel Bacteria and Related Proteins Beyond Discovery into Insecticidal Product Development Phase – GlobeNewswire – Yahoo!Finance

Science, publishing, and career

* Gates Foundation announces open-access publishing venture – Declan Butler – Nature (News section)

The readability of scientific texts is decreasing over time – Pontus Plavén-Sigray – bioRxiv

Amy’s non-microbiology picks

Iron minerals within specific microfossil morphospecies of the 1.88 Ga Gunflint Formation – Kevin Lepot – Nature Communications