Category Archives: Phages and viruses

April 26, 2017

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A series of commentary on the effects of microbiota on vaccines, a fascinating news release about a phage therapy against multi-drug resistant bacterial infection, and can our gut microbes tell us what to eat?

General microbiology

Evaluation of serotypes 5 and 8 capsular polysaccharides in protection against Staphylococcus aureus in murine models of infection – Brian L. Cheng – Human Vaccines & Immunotherapeutics

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? If So, Is There Potential for Efficacious Microbiota-Based Vaccines? – Dan R Littman – Cold Spring Harbor Perspectives in Biology

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? Engaging Our Endogenous Adjuvants – Nicholas Collins1 and Yasmine Belkaid – Cold Spring Harbor Perspectives in Biology

Do the Microbiota Influence Vaccines and Protective Immunity to Pathogens? Issues of Sovereignty, Federalism, and Points-Testing in the Prokaryotic and Eukaryotic Spaces of the Host-Microbial Superorganism – Andrew J. Macpherson – Cold Spring Harbor Perspectives in Biology

Web alert: Microbial therapeutics – Microbial Biotechnology

Human multi-site microbiome

The urinary microbiome and its contribution to lower urinary tract symptoms; ICI-RS 2015 – Marcus J. Drake – Neurourology and Urodynamics

Human gut microbiome

Doctoral Dissertation: The Effects of the Gut Microbiota on the Host Chromatin Landscape – Nicholas Paul Semenkovich – University of Washington, St. Louis

Tissue adaptation: Implications for gut immunity and tolerance – Ana M.C. Faria – Journal of Experimental Medicine

Animal experiments

Doctoral Dissertation, Mouse: The impact of malnutrition on host-microbe interactions in the intestine – Eric Brown – University of British Columbia

Mouse: Deciphering the mechanism of Huang-Lian-Jie-Du-Decoction on the treatment of sepsis by formula decomposition and metabolomics: enhancement of cholinergic pathways and inhibition of HMGB-1/TLR4/NF-κB signaling – Dingqiao Xu – Pharmacological Research

Dysbiosis of intestinal microbiota and decrease in paneth cell antimicrobial peptide level during acute necrotizing pancreatitis in rats – Jing Chen – PLoS One

Commensal bacteria and essential amino acids control food choice behavior and reproduction – Ricardo Leitão-Gonçalves – PLoS Biology

Press: How Gut Bacteria Tell Their Hosts What to Eat – Knvul Sheikh – Scientific American

Press: Are Gut Bacteria Driving Your Cravings? – Shayla Love – Vice

Maternal obese-type gut microbiota differentially impact cognition, anxiety and compulsive behavior in male and female offspring in mice – Annadora J. Bruce-Keller – PLoS One

Animal microbiome

Discovery of tauroursodeoxycholic acid biotransformation enzymes from the gut microbiome of black bears using metagenomics – Can Song – Scientific Reports

Diversity and functions of the sheep faecal microbiota: a multi-omic characterization – Alessandro Tanca – Microbial Biotechnology

New issue of Microbial Biotechnology is available online.

Plant, root and soil microbiome

Microbial communities associated with plants: learning from nature to apply it in agriculture – Fernando Dini Andreote and Michele de Cássia Pereira e Silva- Current Opinion in Microbiology

Life in earth – the root microbiome to the rescue? – Tim H Mauchline, Jacob G Malone – Current Opinion in Microbiology

Unique rhizosphere micro-characteristics facilitate phytoextraction of multiple metals in soil by the hyperaccumulating plant Sedum alfredii – Dandi Hou – Environmental Science & Technology

Water and extremophile microbiome

Doctoral Dissertation: Microbial community variation in an Arctic shelf seafloor – Tan Thi Nguyen – The Arctic University of Norway

Diversity Analysis and Bioresource Characterization of Halophilic Bacteria Isolated from a South African Saltpan – Ramganesh Selvarajan – Molecules

Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis – Daniel Kurth – Scientific Reports

Probiotics

VSL#3 probiotic differently influences IEC-6 intestinal epithelial cell status and function – Benedetta Cinque – Journal of Cellular Physiology

Phages and viruses

Press Release: Novel phage therapy saves patient with multidrug-resistant bacterial infection – University of California, San Diego

Technology

Preprint: Assessing species biomass contributions in microbial communities via metaproteomics – Manuel Kleiner – bioRxiv

Microbes in the news

Are Probiotics the Answer to Acne? – Kristen Fischer – Healthline News

Are the microbes in our gut affecting how fast we age? – Vincent Maffei – OUPblog

Bacteria May be Reason Some Foods Cause Heart Disease, Stroke – Maggie Fox – NBC News

The Slow-Motion Bacteria Buried Deep in the Ocean’s Floor – Veronique Greenwood – The Atlantic

Bacteria from India’s hot springs could help contain oil spills – Dinesh C Sharma – Firstpost

Bacteria causing diarrhoea deaths in children resists key antibiotic – Syed Akbar – The Times of India

Fat rats, slow sperm, and unhealthy bacteria – Lee Evslin – The Garden Island

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 15, 2017

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Few interesting articles for your Saturday morning digest:   Urbanization alters the physicochemical environment: A new study suggests that urban soil archaeal and bacterial communities are not vulnerable to biodiversity loss, whereas global diversity loss of ectomycorrhizal fungi was observed.  Researchers believe they have found a method of hunting for buried landmines and explosive devices using a combination of engineered bacteria and lasers.    And another reason to be engaged in sports activities: a study highlights differences of microbiota and secondary metabolites in elite athletes.

General microbiome

Remote detection of buried landmines using a bacterial sensor – Shimshon Belkin – Nature Biotech

Next-generation approaches to understand and combat the antibiotic resistome – Terence S. Crofts – Nature Reviews

Human Oral Microbiome

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

Human gut microbiome

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

The MS-Associated Gut Microbiome – Sergio E Baranzini – Multiple Sclerosis Journal

Mental Health

Oral treatment with Lactobacillus rhamnosus attenuates behavioral deficits and immune changes in chronic social stress – Aadil Bharwani – BMC Medicine

Animal microbiome

Complete Genome Sequence of Akkermansia glycaniphila Strain PytT, a Mucin-Degrading Specialist of the Reticulated Python Gut – Janneke P. Ouwerkerk – Genome Announcements

Water and extremophile microbiome

Spatial variation in bacterial community in natural wetland-river-sea ecosystems –
Hongxia Zhang – J. of Basic Microbiology

Built environment

Urbanization erodes ectomycorrhizal fungal diversity and may cause microbial communities to converge – Dietrich JE Schmidt -Nature Ecology & Evolution

Prebiotics

Prebiotic evaluation of red seaweed (Kappaphycus alvarezii) using in vitro colon model – DM Bajury – International Journal of Food Sciences and Nutrition

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 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 28, 2017

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A brief digest today, but with several interesting news pieces, including one about 3D-printing bacteria and one about ammonia-digesting bacteria in urinals. Also worth reading are the relationship between human papillomavirus, cancers and the impact of land-based pollution on coral reefs and how clean do you think your home is?

General microbiology

Preprint: Primary souring: a novel bacteria-free method for sour beer production – Kara Osburn – bioRxiv

Human gut microbiome

Low FODMAP in 2017: Lessons learned from clinical trials and mechanistic studies – S. Eswaran – Neurogastroenterology and Motility

Animal experiments

Mouse: Alterations to the Gut Microbiome Impair Bone Strength and Tissue Material Properties – Jason D Guss – Journal of Bone and Mineral Research

Water and extremophile microbiome

Review: New insights into a hot environment for early life – Jianhong Dai – Environmental Microbiology Reports

*A Next-Generation Sequencing Approach to Characterize the Impacts of Land-based Sources of Pollution on the Microbiota of Southeast Florida Coral Reefs – Christopher Staley – Applied and Environmental Microbiology

Effect of salinity on the microbial community and performance on anaerobic digestion of marine macroalgae – Yi Zhang – Journal of Chemical Technology and Biotechnology

Phages and viruses

*Human papillomavirus in cervical cancer and oropharyngeal cancer: One cause, two diseases – Tara A. Berman and John T. Schiller – Cancer

Microbes in the news

On World Tuberculosis Day, Doctors Warn Of New Drug-Resistant Bacteria – Henry Ridgwell – VOA News
Bad breath: Study find array of bacteria when orcas exhale – Phuong Le – ABC News

*Creating materials in a novel way by 3-D printing bacteria – Bob Yirka – Phys.org

Mumbai airport goes green: replaces water in urinals with ammonia-breaking bacteria – DNA web team – DNA India

Gonad-chomping bacteria to be unleashed on dengue virus – Anusha Venkat – Asia Times

Gut bacteria new weapon in fight against asthma – Thoracic Society for Australia and New Zealand Annual Scientific Meeting

*The Dirtiest Things In The Home Don’t Include The Toilet – Zye Angiwan – Immortal News

March 17, 2017

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

General microbiome

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

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

Pregnancy and early life

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

 
Human respiratory microbiome

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

Human gut microbiome

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

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

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

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

Animal experiments

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

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

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

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

Water and extremophile microbiome

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

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

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

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

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

Built environment

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

Probiotics / prebiotics

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

Phages and viruses

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

Bioinformatics

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

Microbes in the news

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