June 19, 2017

Events and jobs

QC Supervisor, Quality Control (Microbiology) – Bausch & Lomb Company Location Seal Beach, CA, US

Microbiology Lab Technician – Apex Life Sciences • Dublin Ohio, OH

General microbiome

Genome-Wide Search for Genes Required for Bifidobacterial Growth under Iron-Limitation – Lanigan N – Front Microbiol

Preprint: Phenotypic consequences of RNA polymerase dysregulation in Escherichia coli – Paramita Sarkar – bioRxiv

EsaB is a core component of the Staphylococcus aureus Type VII secretion system – M. Guillermina Casabona – bioRxiv

Multi-site human microbiome

Dysbiosis in chronic periodontitis: Key microbial players and interactions with the human host – Deng ZL – Sci Rep

Human gut microbiome

Torpor: The Rise and Fall of 3-Monoiodothyronamine from Brain to Gut-From Gut to Brain? – Glossmann HH – Front Endocrinol (Lausanne)

Bacterial Diversity of Intestinal Microbiota in Patients with Substance Use Disorders Revealed by 16S rRNA Gene Deep Sequencing – Xu Y – Sci Rep

Gut Microbiome and Bone: to Build, Destroy, or Both? – Yan J – Curr Osteoporos Rep

From clinical uncertainties to precision medicine: the emerging role of the gut barrier and microbiome in small bowel functional diseases – Marlicz W – Expert Rev Gastroenterol Hepatol

Gut microbiota composition strongly correlates to peripheral insulin sensitivity in obese men but not in women – Most J – Benef Microbes

Animal experiments

Bovine antibodies targeting primary and recurrent Clostridium difficile disease are a potent antibiotic alternative – Hutton ML – Sci Rep

Intestinal metabolites are profoundly altered in the context of HLA-B27 expression and functionally modulate disease in a rat model of spondyloarthropathy – Asquith M – Arthritis Rheumatol

Dietary advanced glycation end products modify gut microbial composition and partially increase colon permeability in rats – Qu W – Mol Nutr Food Res

The scales of the zebrafish: host–microbiota interactions from proteins to populations – Adam R Burns – Curr Opin Microbiol

Plant, root, and soil microbiome

Ecological diversity and co-occurrence patterns of bacterial community through soil profile in response to long-term switchgrass cultivation – He S – Sci Rep

Characterization of microbial communities in Chinese rice wine collected at Yichang city and Suzhou city in China – Lyu Y – J Microbiol Biotechnol

Diversity of endophytic mycobiota of tropical tree Tectona grandis Linn.f.: Spatiotemporal and tissue type effects – Singh DK – Sci Rep

Understanding and exploiting plant beneficial microbes – Finkel OM – Curr Opin Plant Biol

Water and extremophile microbiome

ELIXIR pilot action: Marine metagenomics – towards a domain specific set of sustainable services – Robertsen EM – F1000Res

Built environment

Graphene Nanolayers as a New Method for Bacterial Biofilm Prevention: Preliminary Results – Dybowska-Sarapuk Ł – J AOAC Int

Probiotics / prebiotics

Probiotic guidelines and physician practice: a cross-sectional survey and overview of the literature – Draper K – Benef Microbes


Toward a genetic tool development pipeline for host-associated bacteria – Matthew C Waller – Curr Opin Microbiol

Microbes in the news

Bacteria eaters’ set to transform pig treatment – Lauren Dean – FG|Insight

Bacteria Hysteria

Wash your phones, too – Daily Republic – Onome Johnson



May 29, 2017

What if you can workout while keeping cool with a pleasant smell ? In today’s post, read about researchers from MIT who have developed a ‘breathable workout suit’ using humidity-sensitive E.coli that can take care of cooling you down as you sweat.

Human vaginal microbiome

Early pregnancy vaginal microbiome trends and preterm birth – Stout MJ – Am J Obstet Gynecol.

Human gut microbiome

Chronic consequences on human health induced by microbial pathogens: Growth faltering among children in developing countries – Nataro JP – Vaccine

The gut-brain axis in Parkinson’s disease: Possibilities for food-based therapies – Perez-Pardo P – Eur J Pharmacol.

Animal experiments

Influence of Dietary Avocado on Gut Health in Rats – Paturi G – Plant Foods Hum Nutr.

Transcriptional networks in rodent models support a role for gut-brain communication in neurogenic hypertension: A review of the evidence – Zubcevic J – Physiol Genomics

Plant, root, and soil microbiome

Review: Let the Core Microbiota Be Functional – Lemanceau P – Trends Plant Sci.

An environment friendly engineered Azotobacter can replace substantial amount of urea fertilizer and yet sustain same wheat yield – Umesh K. Bageshwar – Appl Environ Microbiol.
High-resolution analyses reveal structural diversity patterns of microbial communities in Chromite Ore Processing Residue (COPR) contaminated soils – Min X – Chemosphere

Built environment
Pathways in bacterial and archaeal communities dictated by ammonium stress in a high solid anaerobic digester with dewatered sludge – Li N – Bioresour Technol.

Microbes in the news
Experimental athletic shirt uses bacteria to keep you cool during workouts – eParisExtra
Gut Bacteria Changes After Some Weight-Loss Surgeries – tucson.com

February 28, 2017

Events and jobs

Postdoctoral Fellow/Microbiology – University of Tennessee Health Science Center – Memphis, TN

QC Microbiology Analyst – Leidos – FREDERICK, MD US

General microbiome

Preprint: Getting the hologenome concept right: An eco-evolutionary framework for hosts and their microbiomes – Kevin R. Theis – bioRxiv

Preprint: Genome-wide phenotypic analysis of growth, cell morphogenesis and cell cycle events in Escherichia coli – Manuel Campos – bioRxiv

Preprint: Genomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli – Nicole Stoesser – bioRxiv

Preprint: How to name and classify your phage: an informal guide – Evelien M Adriaenssens – bioRxiv

Pregnancy and early life

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

Multi-site human microbiome

A randomised clinical study to determine the effect of a toothpaste containing enzymes and proteins on plaque oral microbiome ecology – S. E. Adams – Scientific reports

Human skin microbiome

Antimicrobials from human skin commensal bacteria protect against Staphylococcus aureus and are deficient in atopic dermatitis – Teruaki Nakatsuji – Science translational medicine

Human vaginal microbiome

Bacterial species colonizing the vagina of healthy women are not associated with race – May A. Beamer – Anaerobes in the microbiome

Human gut microbiome

Combined Signature of the Fecal Microbiome and Metabolome in Patients with Gout – Tiejuan Shao – Frontiers in microbiology

Review: Intestinal microbiome landscaping: insight in community assemblage and implications for microbial modulation strategies – Sudarshan A. Shetty – FEMS-Microbiology reviews

The microbiome and systemic lupus erythematosus – Nurit Katz-Agranov – Immunologic Research

Animal microbiome

Unexplored Archaeal Diversity in the Great Ape Gut Microbiome – Kasie Raymann – mSphere

Plant, root, and soil microbiome

Plant Growth Promoting Bacteria Associated with Langsdorffia hypogaea-Rhizosphere-Host Biological Interface: A Neglected Model of Bacterial Prospection – Érica B. Felestrino – Frontiers in microbiology

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees – Bram Beckers – Microbiome

Plant cultivars imprint the rhizosphere bacterial community composition and association networks – Yuji Jiang – Soil Biology and Biochemistry

Retention and survival of E. coli in stormwater biofilters: Role of vegetation, rhizosphere microorganisms and antimicrobial filter media – G.I. Chandrasena – Ecological Engineering

Nitrogen addition shifts the microbial community in the rhizosphere of Pinus tabuliformis in Northwestern China – Fenglian Lv – PLoS ONE

Investigation of the fungal community structures of imported wheat using high-throughput sequencing technology – Shi Y – PLoS ONE

Players over the Surface: Unraveling the Role of Exopolysaccharides in Zinc Biosorption by Fluorescent Pseudomonas Strain Psd – Anamika Upadhyay – Frontiers in Microbiology
Potential microbial contamination during sampling of permafrost soil assessed by tracers – Toke Bang-Andreasen – Scientific reports

Water and extremophile microbiome

Annual community patterns are driven by seasonal switching between closely related marine bacteria – Christopher S Ward – ISME

Ubiquitous and persistent Proteobacteria and other Gram-negative bacteria in drinking water – Ivone Vaz-Moreira – Science of The Total Environment

Marine-Derived Biocatalysts: Importance, Accessing, and Application in Aromatic Pollutant Bioremediation – Efstratios Nikolaivits – Frontiers in microbiology

Marine Actinobacteria as a source of compounds for phytopathogen control: An integrative metabolic-profiling / bioactivity and taxonomical approach – Luz A. Betancur – PLoS ONE

Archaeal and bacterial communities in deep-sea hydrogenetic ferromanganese crusts on old seamounts of the northwestern Pacific – Shota Nitahara – PLoS ONE

A Proteomic Perspective on the Bacterial Adaptation to Cold: Integrating OMICs Data of the Psychrotrophic Bacterium Exiguobacterium antarcticum B7 – Rafael A. Baraúna – Proteomes

Beneficial Microorganisms for Corals (BMC): proposed mechanisms for coral health and resilience – Raquel Peixoto – Frontiers in microbiology

Science, publishing, and career

Preprint: Preprinting Microbiology – Patrick D. Schloss – bioRxiv

February 15, 2017

Today’s digest features a review on the major mechanisms by which the intestinal microbiota confers protection against infections, studies showing that depression alters gut microbiota while sleep restriction over several consecutive days does not overtly influence the composition of the microbiome.

General microbiome

Microbial communities change in an anaerobic digestion after application of microbial electrolysis cells – Beom Leea – Bioresource Technology

Perspective: Sharpening host defenses during infection: Proteases cut to the chase – Natalie C Marshall – Molecular and cellular proteomics

Review: Recent advances in genetic modification systems for Actinobacteria – Yu Deng – Applied Microbiology and Biotechnology

Preprint: Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica – Zhemin Zhou – bioRxiv

Preprint: In vivo structures of an intact type VI secretion system revealed by electron cryotomography – Yi-Wei Chang – bioRxiv

Eco-evolutionary feedbacks can rescue cooperation in microbial populations – Clara Moreno-Fenoll – Scientific Reports

Pregnancy and early life

Getting organized early in life – Andrea Du Toit – Nature Reviews Microbiology

Infant fungal communities: current knowledge and research opportunities – Tonya L. Ward – BMC Medicine

Human respiratory microbiome

IL-36γ is a crucial proximal component of protective type-1-mediated lung mucosal immunity in Gram-positive and -negative bacterial pneumonia – M A Kovach – MucosalImmunology

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-cystic fibrosis bronchiectasis patients – Michael J. Cox – PLoS ONE

Human skin microbiome

The Role of Cutaneous Microbiota Harmony in Maintaining a Functional Skin Barrier – Hilary E. Baldwin MD – Journal of Drugs in Dermatology

Preprint: Evolutionary and functional implications of hypervariable loci within the skin virome – Geoffrey D. Hannigan – PeerJ

Human vaginal microbiome

Diversity and composition of vaginal microbiota of pregnant women at risk for transmitting Group B Streptococcus treated with intrapartum penicillin – Luiz Fernando Wurdig Roesch – PLoS ONE

Influence of contraceptive choice on vaginal bacterial and fungal microflora – G. Donders – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Human and rat gut microbiome composition is maintained following sleep restrictionShirley L. Zhang – PNAS

Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota – T. Harach – Scientific Reports

Gut to Brain Dysbiosis: Mechanisms Linking Western Diet Consumption, the Microbiome, and Cognitive Impairment – Emily E. Noble – Frontiers in Behavioural Neuroscience

Parkinson’s disease and Parkinson’s disease medications have distinct signatures of the gut microbiome – Erin M. Hill-Burns – Movement Disorders

Persepctive: Diet-induced dysmotility and neuropathy in the gut precedes endotoxaemia and metabolic syndrome: the chicken and the egg revisited – Yvonne Elikplim – The Journal of Physiology

Editorial: Gut–brain axis, psychobiotics, and mental health – Arpit Parmar – Asian Journal of Psychiatry

Comparative study on the in vitro effects of Pseudomonas aeruginosa and seaweed alginates on human gut microbiota – Shaofeng Bai – PLoS ONE

Role of the Gut Microbiome in the Pathogenesis of Obesity and Obesity-Related Metabolic Dysfunction – Kristien E. Bouter – Gastroenterology

Variations in gut microbiota and fecal metabolic phenotype associated with depression by 16S rRNA gene sequencing and LC/MS-based metabolomics – Meng Yu – Journal of Pharmaceutical and Biomedical Analysis

Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome – Ohad Manor – Microbiome

Review: Roles of the intestinal microbiota in pathogen protection – Carles Ubeda – Clinical & Translational Immunology

Antibiotic-Induced Depletion of Anti-Inflammatory Clostridia is Associated with the Development of GVHD in Pediatric Stem Cell Transplant Patients – Tiffany R. Simms-Waldrip – Biology of Blood and Marrow Transplantation

Molecular analysis of the human faecal archaea in a southern Indian population – Sandya B Rani – Journal of Biosciences

Elimination diets’ efficacy and mechanisms in attention deficit hyperactivity disorder and autism spectrum disorder – Verena Ly – European Child & Adolescent Psychiatry

Differences in gut metabolites and microbial composition and functions between Egyptian and U.S. children are consistent with their diets – Shankar V – mSystems
also in the news by ASM

Animal experiments

Comparison of the microbial population in rabbits and guinea pigs by next generation sequencing – Edward J. Crowley – PLoS ONE

Development and validation of a new dynamic in vitro model of the piglet colon (PigutIVM): application to the study of probiotics – Mickaël Alain Fleury – Applied Microbiology and Biotechnology

Effects of dietary nutrient levels on microbial community composition and diversity in the ileal contents of pregnant Huanjiang mini-pigs – Yujiao Ji – PLoS ONE

Nopal feeding reduces adiposity, intestinal inflammation and shifts the cecal microbiota and metabolism in high-fat fed rats – Sofia Moran-Ramos – PLoS ONE
Animal microbiome

Comparative study of the gut microbiome potentially related to milk protein in Murrah buffaloes (Bubalus bubalis) and Chinese Holstein cattle – Jiachao Zhang – Scientific Reports

Meta-analysis to estimate the load of Leptospira excreted in urine: beyond rats as important sources of transmission in low-income rural communities – Veronica Barragan – BMC Research Notes

Plant, root, and soil microbiome

The microbe-secreted isopeptide poly-γ-glutamic acid induces stress tolerance in Brassica napus L. seedlings by activating crosstalk between H2O2 and Ca2+ – Peng Lei – Scientific Reports

Paenibacillus polymyxa NSY50 suppresses Fusarium wilt in cucumbers by regulating the rhizospheric microbial community – Lu Shi – Scientific Reports

Community-level physiological profiling analyses show potential to identify the copiotrophic bacteria present in soil environments – Salvador Lladó – PLoS ONE

Pseudomonas protegens CS1 from the lemon phyllosphere as a candidate for citrus canker biocontrol agent – G. Michavila – Plant biology

Role and Regulation of ACC Deaminase Gene in Sinorhizobium meliloti: Is It a Symbiotic, Rhizospheric or Endophytic Gene? – Alice Checcucci – Frontiers in Genetics

Use of endophytic and rhizosphere bacteria to improve phytoremediation of arsenic-contaminated industrial soils by autochthonous Betula celtiberica – Victoria Mesa – Applied and Environmental Microbiology

Bioaugmentation with bacteria selected from the microbiome enhances Arthrocnemum macrostachyum metal accumulation and tolerance – Salvadora Navarro-Torre – Marine Pollution Bulletin

Proteotyping of laboratory-scale biogas plants reveals multiple steady-states in community composition – F. Kohrs – Anaerobe

Soil microbial communities alter leaf chemistry and influence allelopathic potential among coexisting plant species – Scott J. Meiners – Oecologia

Review: Abiotic stress responses and microbe-mediated mitigation in plants: The omics strategies – Kamlesh K. Meena – Frontiers in Plant Science

Complete genome analysis of Serratia marcescens RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants – Abdur Rahim Khan – PLoS ONE

Wildfire impact: Natural experiment reveals differential short-term changes in soil microbial communities – Miranda T. Prendergast-Miller – Soil Biology and Biochemistry

Diverse microbial communities in non-aerated compost teas suppress bacterial wilt – W. K. Mengesha – World Journal of Microbiology and Biotechnology

Fumigation with dazomet modifies soil microbiota in apple orchards affected by replant disease – Lidia Nicola – Applied Soil Ecology

Arbuscular mycorrhiza enhance the rate of litter decomposition while inhibiting soil microbial community development – Heng Gui – Scientific Reports

Apple replant disorder of Pingyitiancha rootstock is closely associated with rhizosphere fungal community development – Jian Sun – Jounral of Phytopathology

Changes in soil bacterial communities in an evergreen broad-leaved forest in east China following 4 years of nitrogen addition – Jun Cui – Journal of Soils and Sediments

Distinct biogeographic patterns for archaea, bacteria, and fungi along the vegetation gradient at the continental scale in eastern China – Bin Ma – mSystems

Insight into the effects of different cropping systems on soil bacterial community and tobacco bacterial wilt rate – Jiaojio Niu – Journal of Basic Microbiology
Water and extremophile microbiome

Dimethylsulfoniopropionate biosynthesis in marine bacteria and identification of the key gene in this process – Andrew R. J. Curson – Nature Microbiology

Metagenomic survey of the taxonomic and functional microbial communities of seawater and sea ice from the Canadian Arctic – Etienne Yergeau – Scientific Reports

Response of deep subsurface microbial community to different carbon sources and electron acceptors during ~two months incubation in microcosms – Lotta Purkamo – Frontiers in Microbiology

Bacterial community dynamics are linked to patterns of coral heat tolerance – Maren Ziegler – Nature Communications

Preprint: Habitat generalists or specialists, insights from comparative genomic analyses of Thermosipho lineages – Thomas H.A. Haverkamp – bioRxiv

Culture scale-up and immobilisation of a mixed methanotrophic consortium for methane remediation in pilot-scale bio-filters – Obulisamy Parthiba Karthikeyan – Environmental technology

Effect of different enrichment strategies on microbial community structure in petroleum-contaminated marine sediment in Dalian, China – Chao Chen – Marine Pollution Bulletin

Microbial catabolic diversity in and beyond the rhizosphere of plant species and plant genotypes – Karst M. Brolsmaa – Pedobiologia

Preprint: Shifting microbial communities sustain multi-year iron reduction and methanogenesis in ferruginous sediment incubations – Marcus S Bray – bioRxiv


A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems – Marko Budinich – PLoS ONE

Modelling functional resilience of microbial ecosystems: Analysis of governing processes – Sara König – Environmental Modelling & Software

An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data – W. Duncan Wadsworth – BMC Bioinformatics


Metabolomics: A Primer – Xiaojing Liu – Trends in biochemical sciences

Fluorescence Lectin Bar-Coding of Glycoconjugates in the Extracellular Matrix of Biofilm and Bioaggregate Forming Microorganisms – Thomas R. Neu – Microorganisms

Microbes in the news

Experts reveal how the microbiome in your gut is linked to weight gain and health disorders – Leah Hardy – MailOnline
Will cities of the future embrace bacteria? – Starre Vartan- MNN.com

Microbes on the market

FDA Turmoil, Biology Mystery On List Of Hurdles For Microbiome Drugs – Ben Fidler – exome

Science, publishing, and career

FICUS JGI-NERSC Microbiome Data Science Call for Proposals (Open till 1st of March)