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)

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