June 10, 2017

Jobs and events

Two tenure-track assistant professor or associate professors – Department of Plant and Microbial Biology – College of Biological Sciences, University of Minnesota

Sign up for the webinar by Edward Messick, GENEWIZ – Topic: Metagenomics for Biomarker Discovery: Applications in Precision Medicine – Webinar date and time: June 14, 2017 at 5 PM


General microbiome

Ferrous Iron Efflux Systems in Bacteria – H Pi – Metallomics

Metagenomics of microbial and viral life in terrestrial geothermal environments – A Strazzulli – Reviews in Environmental Science and Bio/Technology

Bacterial Infections in Neonates Following Mupirocin-Based MRSA Decolonization: A Multicenter Cohort Study – R Pierce – Infection Control & Hospital Epidemiology


Human gut microbiome

Interindividual variability of soil arsenic metabolism by human gut microbiota using SHIME model –  N Yin – Chemosphere

Report: Daily Changes in Composition and Diversity of the Intestinal Microbiota in Patients with Anorexia Nervosa: A Series of Three Cases – SC Kleiman – European Eating Disorders Review


Animal experiment

A Targeted Metabolomics Analysis Identifies Intestinal Microbiota-Derived Urinary Biomarkers of Colonization Resistance in Antibiotic-Treated Mice – ME Obrenovich – Antimicrobial Agents and Chemotherapy


Animal microbiome

Molecular dialogues with the microbiota: Lessons from the zebrafish intestine – K Guillemin – Mechanisms of Development


Plant, root and soil microbiome

The nodule microbiome; N2-fixing rhizobia do not live alone  – P  Martínez-Hidalgo – Phytobiomes Journal

Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity – X Zhang – Global Change Biology

Turnover of carbon and phosphorus in the microbial biomass depending on phosphorus availability – M Spohn – Soil Biology and Biochemistry

Effect of soil preparation techniques on the biochemical properties and microbial communities of a citrus orchard after replanting and conversion into organic management – A Pérez-Piqueres – Applied Soil Ecology


Water microbiome and extremophile

Review: The Vulnerability and Resilience of Reef-Building Corals – HM Putnam – Current Biology

Bacterial and archaeal community structure of pan-Arctic Ocean sediments revealed by pyrosequencing – X Lin – Acta Oceanologica Sinica

Genetic diversity of nitrate reducing bacteria in marine and brackish water nitrifying bacterial consortia generated for activating nitrifying bioreactors in recirculating aquaculture systems – PG Preena – Aquaculture Research



Integrated transcriptomic, proteomic and epigenomic analysis of Plasmodium vivax salivary-gland sporozoites – A Jex – bioRxiv

Discrimination of haloarchaeal genera using Raman spectroscopy and robust methods for multivariate data analysis – NE Dina – Journal of Raman Spectroscopy



Comparative metabolomics in vanilla pod and vanilla bean revealing the biosynthesis of vanillin during the curing process of vanilla –  F Gu – AMB Express



A highly specific phage defense system is a conserved feature of the Vibrio cholerae mobilome – BJ O’ Hara – PLoS Genetics


Built environment microbiome

Warm and wet: robust lipase-producing bacteria from the indoor environment – K Tanner – bioRxiv

Impacts of biostimulation and bioaugmentation on the performance and microbial ecology in methanogenic reactors treating purified terephthalic acid wastewater – M Liu – Water Research


More microbes

Viral Encephalitis of Unknown Cause: Current Perspective and Recent Advances – PGE Kennedy – Viruses

Protozoa and microbiome  – SL Burgess – Infection and Immunity

Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens  – JE Heindl – bioRxiv

Intercellular communication via the comX-Inducing Peptide (XIP) of Streptococcus mutans – J Kaspar – bioRxiv

Hammondia hammondi has a developmental program in vitro that mirrors its stringent two host life cycle – SL Sokol – bioRxiv


Microbes in news

Engineering ‘good’ bacteria to kill bad ones – The Straits Times

White or wholemeal? It depends on your gut bacteria – A Middleton – Cosmos

Ixcela Announces Partnership with ORACLE TEAM USA to Improve Athletes’ Internal Health and Performance – Business Wire

New Study Finds Gut Bacteria May Inhibit Cancer Drugs – K Lant – Futurism

Therapy could stop superbugs on farms – P Ghosh – BBC News

SHU students travel to present phages research – P Parise – Setonian Online

June 4, 2017

Some exciting papers in the sections- General microbiome & Microbes in news, to get you through Sunday!

General microbiome

The 5D Framework: A Clinical Primer for Fecal Microbiota Transplantation to Treat Clostridium difficile infection – JR Allegretti – Gastrointestinal Endoscopy

Abatement of AO7 in a divided microbial fuel cells by sequential cathodic and anodic treatment powered by different microorganisms – G Riccobono – Journal of Electroanalytical Chemistry

THE MICROBIOME AND TRANSFUSION IN CANCER PATIENTS – H Goubran – Transfusion and Apheresis Science

« Olsenella congonensis» sp.nov., identified in human stool sample – M Bilen – New Microbes and New Infections

Description of “Blautia phocaeensis” sp.nov., and “Lachnoclostridium edouardi” sp. nov., isolated from healthy fresh stools of Saudii Arabia bedouins by culturomics – SI Traore  – New Microbes and New Infections

Sulfur-driven iron reduction coupled to anaerobic ammonium oxidation – P Bao – Environmental Science and Technology


Animal microbiome

Diversity and composition of cultivable gut bacteria in an endemic island bird and its mainland sister species – E Lobato – Symbiosis

Modulation of ruminal fermentation profile and microbial abundance in cows fed diets treated with lactic acid, without or with inorganic phosphorus supplementation – E Mickdam – Animal Feed Science and Technology

A pea (Pisum sativum L.) seed albumin extract prevents colonic DSS induced dysbiosis in mice – I Aranda-Olmedo – Journal of Functional Foods


Human respiratory microbiome

The Respiratory Microbiome: Beyond the Culture – E Monsó – Archivos de Bronconeumología

WS03.7 Coexistence of prey and predator bacteria in cystic fibrosis lung microbiota – J. de Dios-Caballero – Journal of Cystic Fibrosis


Human gut microbiome

The gut bacterium and pathobiont Bacteroides vulgatus activates NF-κB in a human gut epithelial cell line in a strain and growth phase dependent manner – P Ó Cuív – Anaerobe

Chlorogenic acid versus amaranth’s caffeoylisocitric acid – Gut microbial degradation of caffeic acid derivatives – M Vollmer – Food Research International

Consumption effect of a synbiotic beverage made from soy and yacon extracts containing Bifidobacterium animalis ssp. lactis BB-12 on the intestinal polyamine concentrations in elderly individuals – MSJ Manzoni – Food Research International

Review: Effect of diet and gut environment on the gastrointestinal formation of N-nitroso compounds: A review – J Kobayashi – Nitric Oxide

Atopic dermatitis and food sensitization in South African toddlers : Role of fiber and gut microbiota – M Mahdavinia – Annals of Allergy, Asthma & Immunology


Plant, root and soil microbiome

Significant Impacts of Increasing Aridity on the Arid Soil Microbiome – JW Neilson – mSystems

Consequences of tropical forest conversion to oil palm on soil bacterial community and network structure – SA Wood – Soil Biology and Biochemistry

The response of archaeal species to seasonal variables in a subtropical aerated soil: insight into the low abundant methanogens – W Xie – Applied Microbiology and Biotechnology

Relative roles of competition, environmental selection and spatial processes in structuring soil bacterial communities in the Qinghai-Tibetan Plateau – J Zhou – Applied Soil Ecology

Isolation and identification of endophytic bacteria with plant growth promoting and biocontrol potential from oak trees – F Tashi-Oshnoei – Forest Pathology

Illumina-Based Sequencing Analysis Directed Selection for Actinobacterial Probiotic Candidates for Banana Plants – X Du – Probiotics and Antimicrobial Proteins

The influence of land use intensity on the plant-associated microbiome of Dactylis glomerata L. – J Estendorfer – Frontiers in Plant Science


Water microbiome and extremophiles

An overlooked nitrogen loss linked to anaerobic ammonium oxidation in estuarine sediments in China – XR Yang – Journal of Soils and Sediments


Food microbiology

Evolution of microbiota during spontaneous and inoculated Tonda di Cagliari table olives fermentation and impact on sensory characteristics – R Comunian – LWT-Food Science and Technology

PCR-DGGE markers for qualitative profiling of microbiota in raw milk and ripened cheeses – B Nalepa – LWT-Food Science and Technology

Identification of enzymatic activities involved in agave fructan consumption by Bifidobacterium longum subsp. infantis ATCC 15697 – E Cuevas-Juárez – Journal of Functional Foods



Photodynamic Therapy With Methylene Blue for Skin Ulcers Infected With Pseudomonas aeruginosa and Fusarium spp – C Aspiroz – Actas Dermo-Sifiliográficas



Antibacterial efficacy of nisin, bacteriophage P100 and sodium lactate against Listeria monocytogenes in ready-to-eat sliced pork ham – ACL Figueiredo – Brazilian Journal of Microbiology


More microbes

Spore forming bacteria in beer: occurrence, diversity, presence of hop resistance genes and fate in alcohol-free and lager beers – ARG Munford – Food Control

Survey of pathogens in threatened wild red-tailed Amazon parrot (Amazona brasiliensis) nestlings in Rasa Island, Brazil – FF Vaz – Brazilian Journal of Microbiology

Species specific substrates and products choices of 4-O-acetyltransferase from Trichoderma brevicompactum – S Sharma – Enzyme and Microbial Technology

Review: The Goldilocks model of immune symbiosis with Mycobacteria and Candida colonizers – RT Robinson – Cytokine

Immunological and epidemiological factors affecting candidiasis in HIV patients beginning antiretroviral therapy in an Asian clinic – EAT Wulandari – Archives of Oral Biology

Diversity and Ecology of and Biomineralization by Magnetotactic Bacteria – W Lin – Environmental Microbiology Reports


Microbes in news

Man Dies After His Tattoo Gets Infected with Ocean Bacteria – R Rettner – Live Science

Accelerated breeding of mutant bacteria may choke space race – J Seidel – News Corp Australia Network

Microgravity Can Permanently Mutate Bacteria to Make Them Faster Breeders –  D Nield – Science Alert

Vaginal bacteria can inhibit sexual transmission of Zika virus – Healio

Bacteria levels subside, Spring Lake beach reopens – R Zimmer – App.com

Meet C. diff, the gross bacteria on the soles of your shoes – E Roberts – Today

The Microscopic World of Bacteria Comes to Life with Sculpture – CR  Fernández – Labiotech

New Microbiology Data Reinforce Activity of Paratek’s Omadacycline Against Pathogens of Importance in Respiratory, Skin and Urinary Tract Infections – Paratek – Nasdaq Globe News Wire

A Traumatic Experience Can Reshape Your Microbiome – S Neilson – Huffington Post

Zymo Research to Launch Three New Kits for Microbiome Research at ASM Microbe 2017 – Zymo Research Corp. – PR Newswire

The gut microbiota plays key role in diabetes treatment – N Marriott –  Drug Target Review

In a first, Human Microbiome Project Launched in Northeast India! – TNT News

Metformin joins forces with gut microbes to improve blood sugars, new study finds – C Bienvenu – Diabetes.co.uk



May 27, 2017

Today’s digest has some great papers in the section-Plant, root and soil microbiome

General microbiome

Concentration and Viability of Bacterial Aerosols Associated with Weather in Asian Continental Outflow: Current Understanding – D Zhang – Aerosol Science and Engineering

Specific Virus-Host Genome Interactions Revealed By Tethered Chromosome Conformation Capture – H Li – bioRxiv

Metabolic Integration of Bacterial Endosymbionts through Antimicrobial Peptides – P Mergaert – Trends in Microbiology

Isolation and Characterization of Phenol-Degrading Psychrotolerant Yeasts – N Filipowicz – Water, Air, & Soil Pollution


Animal microbiome

Impact of dietary Moringa oleifera leaves on intestinal pathogenic load and histological structure of growing rabbits raised under heat-stress conditions – AY El-Badawi – Animal Production Science

CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice – KN Chitrala – European Journal of Immunology

Meta-analysis To Define a Core Microbiota in the Swine Gut – DB Holman – mSystems


Plant, root and soil microbiome

Let the Core Microbiota Be Functional – P Lemanceau – Trends in Plant Science

Phytobiomes – Editor-in-Chief: CA Young

Bio-mining the forest ecosystem of North East India for identification of antimicrobial metabolites from fungi through submerged fermentation – SI Devi – Bioresource Technology

Kisameet Glacial Clay: an Unexpected Source of Bacterial Diversity – SL Svensson – mBio

Microbiome-on-a-Chip: New Frontiers in Plant–Microbiota Research – CE Stanley – Trends in Microbiology

Soil microbial properties as affected by short-term contrasting tillages and cropping systems in a rainfed agro-ecosystem of Northern Odisha – KN Mishra – Evolutionary Ecology

Comparison of rhizosphere properties as affected by different Bt- and non-Bt-cotton (Gossypium hirsutum L.) genotypes and fertilization – M Ahamd – Environmental Monitoring and Assessment

Soil fungal diversity in natural grasslands of the Tibetan Plateau: associations with plant diversity and productivity – T Yang – New Phytologist

Bacterial Microbiome and Nematode Occurrence in Different Potato Agricultural Soils – JD Castillo – Microbial Ecology

Lipopeptides produced by B. amyloliquefaciens NJN-6 altered the soil fungal community and non-ribosomal peptides genes harboring microbial community – J Yuan – Applied Soil Ecology

The differential impact of a native and a non-native ragwort species (Senecioneae) on the first and second trophic level of the rhizosphere food web – P Harkes – Oikos


Food microbiology

Impact of thistle rennet from Carlina acanthifolia All. subsp. acanthifolia on bacterial diversity and dynamics of a specialty Italian raw ewes’ milk cheese – F Cardinali – International Journal of Food Microbiology

High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions – CJ Doyle – International Journal of Food Microbiology


Built environment microbiology

Direct treatment of high-strength soft drink wastewater using a down-flow hanging sponge reactor: performance and microbial community dynamics – J Liao – Applied Microbiology and Biotechnology



Comparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium – R Kumar – mSystems

Fermentation quality, in vitro digestibility and aerobic stability of total mixed ration silages prepared with whole-plant corn (Zea mays L.) and hulless barley (Hordeum vulgare L.) straw – X Yuan – Animal Production Science

Investigation of compatible solutes synthesis and transport of Virgibacillus halodenitrificans PDB-F2 with complete genome analysis – Y Zhou – International Biodeterioration & Biodegradation

An 18S rRNA Workflow for Characterizing Protists in Sewage, with a Focus on Zoonotic Trichomonads – JM Maritz – Microbial Ecology


More microbes

HIV Persistence Alters CXCR4 Expression Patterns In OP9-DL1-Mediated Differentiation Of In Vitro Infected Human Cord Blood CD34+ Cells – T Tsukamoto – bioRxiv

Bacterial Virus Ontology; Coordinating across Databases – C Hulo – MDPI


Microbes in news

New insights into the ancestors of all complex life – University of Bristol – News

How a Usually Harmless Bacteria Ended Up Killing 18 People in Wisconsin – S Zhang – The Atlantic

Where you can check beaches for bacteria – Daily Herald

Beware: How to avoid rare flesh-eating bacteria in Chesapeake Bay – M Basch – WTOP

Gut Microbiome Affects Two Nervous System Diseases – AL Komarrof – Journal Watch

Solution to many global challenges may be right under our feet – G Dufficy – AgriLand

Bugging cancer: gut bacteria and the big C – V Martinez – The Irish Times


Non-microbiology picks

Marginal Returns And Levels Of Research Grant Support Among Scientists Supported By The National Institutes Of Health – MS Lauer – bioRxiv

Conservation and restoration practices in humid climates – D Tejeda Sartorius – CAB Direct

May 15, 2017

General microbiome

Plastics in the North Atlantic garbage patch: A boat-microbe for hitchhikers and plastic degraders – D Didier – Science of the Total Environment

Biodegradation and metabolic fate of levofloxacin via a freshwater green alga, Scenedesmus obliquus in synthetic saline wastewater – JQ Xiong – Algal Research

Ionic liquid-based reagents improve the stability of midterm fecal sample storage – L Hao – Journal of Microbiological Methods

Aerobic vaginitis: no longer a stranger – GGG Donders – Research in Microbiology –

The antibiotic resistome: gene flow in environments, animals and human beings – Y Hu – Frontiers of Medicine


Human respiratory microbiome

Neutrophil Extracellular Traps are associated with disease severity and microbiota diversity in Chronic Obstructive Pulmonary Disease – AJ Dicker – Journal of Allergy and Clinical Immunology

Airway Microbial Diversity is Inversely Associated with Mite-Sensitized Rhinitis and Asthma in Early Childhood – CY Chiu – Scientific Reports

Determination of nasal and oropharyngeal microbiomes in a multicenter population-based study – findings from Pretest 1 of the German National Cohort – MK Akmatov – Scientific Reports

Compositionally and functionally distinct sinus microbiota in chronic rhinosinusitis patients have immunological and clinically divergent consequences – EK Cope – Microbiome


Animal microbiome

Response of turkeys fed wheat-barley-rye based diets to xylanase supplementation – G González Ortis – Animal Feed Science and Technology

Bifidobacterium CECT 7765 modulates early stress-induced immune, neuroendocrine and behavioral alterations in mice – A Moya Pérez – Brain, Behavior, and Immunity


Water and extremophile

UV-Resistant Actinobacteria from High-Altitude Andean Lakes: Isolation, Characterization and Antagonistic Activities – MC Rasuk – Photochemistry and Photobiology



A Tunable Protein Oscillator Controls Directional Movements In Myxococcus xanthus – M Guzzo – bioRxiv

Uncovering The Drivers Of Animal-Host Microbiotas With Joint Distribution Modeling – JR Bjork – bioRxiv


Microbes in news

Hospital superbugs – The Hans India

Market pressures and inadequate production are hampering access to essential antibiotics – EurekAlert

Learning the rules of antibiotics to make old drugs work on new bugs –  D Gitig – ARS Technica

Does Cooking Kill Probiotics? – KDA Traegner – Care2

Research team hopes to reduce size of tsunami using bacteria – The Mainichi

Antibiotic-resistant bacteria predate dinosaurs study reports – J Scalise – Science Recorder

Vexed childhood likely to cause irritable bowel syndrome (IBS) – NewsGram

Study suggests link between imbalanced gut microbiome and systemic sclerosis – UCLA Health

Microbiome leader Professor Borody joins researchers at the China Microbiota Transplantation Conference – MENAFN

How doctors could use viruses to kill drug-resistant bacteria – CTV News

Microbiologists find bugs, bacteria – and poo – lurking inside the UK’s cars – J Watkiss – Cambridge News

#Flint: As Mich. Gov. Snyder Signs $100,000,000 in Aid Into Law, Residents Warned Water Filters Harbor Bacteria – M Judge – The Root

Rutgers Researchers See Paper as a Defense Against Bacteria – J Murtha – Tap Into

Bacteria find clarified – S Silaitoga – The Fiji Times Online

The Filthiest, Most Bacteria Infested Places In Your Kitchen – Sky Valley Chronicle

May 1, 2017

General microbiome

From Gene Annotation to Function Prediction for Metagenomics – F Sharifi – Protein Function Prediction

*Review: A critical assessment of the “sterile womb” and “in utero colonization” hypotheses: implications for research on the pioneer infant microbiome – ME Perez-Muñoz – Microbiome

Collateral damage during antibiotic treatment of C. difficile infection in the aged host: insights into why recurrent disease happens – JH Shin – Gut Microbes


Human oral microbiome

Oral Treponeme Major Surface Protein: Sequence Diversity and Distributions within Periodontal Niches – M You – Molecular Oral Microbiology


Human gut microbiome

Reduction in fecal microbiota diversity and short-chain fatty acid producers in Methicillin-resistant Staphylococcus aureus infected individuals as revealed by PacBio single molecule, real-time sequencing technology – J Zhao – European Journal of Clinical Microbiology & Infectious Diseases

Gut Check: The evolution of an educational board game – DA Coil – PLoS Biology

From sensing to shaping microbiota: insights into the role of NOD2 in intestinal homeostasis and progression of Crohn’s Disease – I Balasubramanian – Am. J. Physiol. Gastrointest. Liver Physiol.

Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naïve Parkinson’s disease patients – JR Bedorf – Genome Medicine


Animal microbiome

Progressive response of large intestinal bacterial community and fermentation to the stepwise decrease of dietary crude protein level in growing pigs – Y Peng – Applied Microbiology and Biotechnology

Repeated inoculation of cattle rumen with bison rumen contents alters the rumen microbiome and improves nitrogen digestibility in cattle – GO Ribeiro – Scientific Reports

Impact and consequences of polyphenols and fructooligosaccharide interplay on gut microbiota in rats – CJ Zheng – Food & Function


Plant, root and soil microbiome

Not just browsing: an animal that grazes phyllosphere microbes facilitates community heterogeneity – R O′ Rorke – ISME

Environmental Metabarcoding Reveals Contrasting Belowground and Aboveground Fungal Communities from Poplar at a Hg Phytomanagement Site –  A Durand – Microbial Ecology

Understory Dwarf Bamboo Affects Microbial Community Structures and Soil Properties in a Betula ermanii Forest in Northern Japan – B Kong – Microbes & Environments

Effects of root exudates on denitrifier gene abundance, community structure and activity in a micro-polluted constructed wetland – H Wu – Sci. Total Environ

Contribution of native phosphorous-solubilizing bacteria of acid soils on phosphorous acquisition in peanut (Arachis hypogaea L.) – M Pradhan – Protoplasma



Aggregation and Adhesion Activity of Lactobacilli Isolated from Fermented Products In Vitro and In Vivo: a Potential Probiotic Strain – S Grigoryan – Probiotics and Antimicrobial Proteins


Built environment microbiology

Three-stage anaerobic co-digestion of food waste and horse manure – J Zhang – Scientific Reports


Microbes in news

Undeveloped microbiomes make infants more prone to illness – R Saxena – ARS Technica

Being a guinea pig for science can be a long, slow slog – B Jefferson – SCPR

Pharma pollution fuels resistance to antibiotics, bacteria turns super bug – TNN – The Times of India

Cleaning up Iowa’s beaches – E Jordan – The Gazette

Augusta hospital adopts test to help find treatment for some patients quicker – S Turner – Aiken Standard

Only a superweapon can kill superbacteria, and humanity finally found it – W Nicol – Digital Trends

‘Lab in a cell’ helps crack code on chlamydia – R Shore –  Edmonton Journal



April 14, 2017

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



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 4, 2017

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



*ReviewBioelectrochemical 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

*ReviewShapeshifting 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