February 20, 2017

This Monday we have some quite interesting news about microbes! Microbes found inside giant crystals in caves in Chihuahua, Mexico, may have survived there for tens of thousands of years, while meadows of underwater seagrass plants might lower levels of harmful bacteria in nearby ocean waters making the whole ecosystem — from corals to fish to humans — healthier. Enjoy your reading..

Pregnancy and early life

Adenoid bacterial colonization in a paediatric population – João Subtil – European Archives of Oto-Rhino-Laryngology

Human gut microbiome

Review: NLRP6: A Multifaceted Innate Immune Sensor – Maayan Levy – Trends in Immunology

Prebiotic inulin-type fructans induce specific changes in the human gut microbiota – Doris Vandeputte – Gut

Gut microbial profile is altered in primary biliary cholangitis and partially restored after UDCA therapy – Ruqi Tang – Gut

Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial – Sudarshan Paramsothy – The Lancet

Reinforcement of intestinal epithelial barrier by arabinoxylans in overweight and obese subjects: A randomized controlled trial: Arabinoxylans in gut barrier – Bouke N. Salden – Clinical Nutrition

Diet-induced obesity, gut microbiota and bone, including alveolar bone loss – Sathima Eaimworawuthikul – Archives of Oral Biology

Animal experiments

Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha Diversity – Robert S. Thompson – Frontiers in  Behavioral Neuroscience

Plant, root, and soil microbiome

Plant community and nitrogen deposition as drivers of α- and β-prokaryotic diversity in reconstructed oil-sands soils and natural boreal forest soils – Jacynthe Masse – Applied and Environmental Microbiology

Plant-microbial association in petroleum and gas exploration sites in the state of Assam, north-east India—significance for bioremediation – Hemen Sarma – Environmental Science and Pollution Research

The choice of the DNA extraction method may influence the outcome of the soil microbial community structure analysis – Sylwia Zielińska – Microbiology Open

Water and extremophile microbiome

Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes, and invertebrates – Joleah B. Lamb – Science

Phages and viruses

Cyanophage-encoded lipid-desaturases: oceanic distribution, diversity and function – Sheila Roitman – bioRxiv

Techniques

Effects of gelling agent and extracellular signaling molecules on the culturability of marine bacteria – Anita Mac Rygaard – Applied and Environmental Microbiology

A tool named Iris for versatile high-throughput phenotyping in microorganisms – George Kritikos – Nature Microbiology

Microbes in the news 

Microbes survived inside giant cave crystals for up to 50,000 years – Science News

Three-way dance between herbivores, plants and microbes unveiled  – Phys.org

Synthetic antibiotic developed by Sask. researchers to combat drug-resistant bacteria – CBC News

Salmonella ‘can kill cancer’: How bacteria that cause food poisoning could be used to attack tumour cells – Colin Fernandez for Daily Mail, UK

Brazilian peppertree packs power to knock out antibiotic-resistant bacteria – Science Daily

Bacteria Hysteria

Drug-resistant deadly bacteria more widespread than previously thought, study finds – News Medical

 

February 19, 2017.

A light digest for today’s Sunday morning. A variety of human microbiome papers and a review on the evolution of antimicrobial resistance.

Human respiratory microbiome

Community analysis of dental plaque and endotracheal tube biofilms from mechanically ventilated patients. Poala J Marino. Journal of Critical Care.

Human nearly-sterile sites

Short communication: Epicardial Adipose Tissue Microbial Colonization and Inflammasome Activation in Acute Coronary Syndrome. Daniela Pedicino. International Journal of Cardiology.

Human gut microbiome

Microbiota Disruption Induced by Early Use of Broad Spectrum Antibiotics is an Independent Risk Factor of Outcome after Allogeneic Stem Cell Transplantation. Daniela Weber.
Biology of Blood and Marrow Transplantation.

Nutritional stimulation of commensal oral bacteria suppresses pathogens: the prebiotic concept. Vera Slomka. Clinical Periodontology.

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota. A. Sloan Devlin. Cell Host & Microbe.

Animal experiments

Host Genotype and Gut Microbiome Modulate Insulin Secretion and Diet-Induced Metabolic Phenotypes. Julia H. Kreznar. Cell Reports.

Microbes in the environment

Attached and Suspended Denitrifier Communities in Pristine Limestone Aquifers Harbor High Fractions of Potential Autotrophs Oxidizing Reduced Iron and Sulfur Compounds. M Herrmann. Microbial Ecology.

Human influence and biotic homogenization drive the distribution of Escherichia coli virulence genes in natural habitats. Adriano Cabal. Microbiology Open.

Antibacterial Activities of Bacteria Isolated from the Marine Sponges Isodictya compressa and Higginsia bidentifera Collected from Algoa Bay, South Africa. Relebohile Matthew Matobole. Marine Drugs.

Food microbiology

Bacterial ecology of artisanal Minas cheeses assessed by culture-dependent and -independent methods. Luana Martins Perin. Food Microbiology.

Perspective: New insights on the use of wine yeasts. Francesca Comitini. Current Opinion in Food Science.

Phages and viruses

Pre-print: Viral coinfection is shaped by host ecology and virus-virus interactions across diverse microbial taxa and environments. Samuel L. Díaz Muñoz. bioRxiv.

Biotechnology

Virulence Inhibitors from Brazilian Peppertree Block Quorum Sensing and Abate Dermonecrosis in Skin Infection Models. Amelia Muhs. Scientific Reports.

Evolution

Review: Epistasis and the Evolution of Antimicrobial Resistance. Alex Wong. Frontiers Microbiology.

February 18, 2017

Events and jobs

Assistant Professor – Pathogen and Microbiome Institute at Northern Arizona University

Assistant Professor – Biochem & Microbiology at Rutgers University

Expert Panel Discussions to be Highlight of Agenda at the 3rd Annual Translational Microbiome Conference – prweb

General microbiome

Neutral and niche dynamics in a synthetic microbial community -NJ Cira – bioRxiv

Human respiratory microbiome

Indoor fungal diversity in primary schools may differently influence allergic sensitization and asthma in children – João Cavaleiro Rufo – Pediatric Allergy Immunology

Human gut microbiome

Mining the Human Gut Microbiota for Immunomodulatory Organisms – Naama Geva-Zatorsky – Cell

Animal experiments

The enteric nervous system promotes intestinal health by constraining microbiota composition – Annah S. Rolig – PLoS Biology

Biologists control gut inflammation by altering the abundance of resident bacteria – Science Daily

Drunk bugs: Chronic vapour alcohol exposure induces marked changes in the gut microbiome in mice – Veronica L. Peterson – Behavioural Brain Research

Mouse model of alcohol abuse shows microbiome changes – Taconic

Feeding a High Concentration Diet Induces Unhealthy Alterations in the Composition and Metabolism of Ruminal Microbiota and Host Response in a Goat Model – Canfeng Hua – Frontiers in Microbiology

Animal microbiome

Impact of levels of total digestible nutrients on microbiome, enzyme profile and degradation of feeds in buffalo rumen – Anju Kala – PLoS ONE

Immune system stimulation by the gut symbiont Frischella perrara in the honey bee (Apis mellifera) – Olivier Emery – Molecular Ecology

Integrating gut microbiota immaturity and disease-discriminatory taxa to diagnose the initiation and severity of shrimp disease – Jinbo Xiong – Environmental Microbiology

Plant, root, and soil microbiome

Linking soil biology and chemistry using bacterial isolate exometabolite profiles – Tami L Swenson – bioRxiv

Ecological and conventional viticulture gives rise to distinct fungal and bacterial microbial communities in vineyard soils – M. Likar – Applied Soil Ecology

Effects of land use on soil microbial biomass, activity and community structure at different soil depths in the Danube floodplain – J.P. van Leeuwen – European Journal of Soil Biology

*Review: How do Plants-Having Different Exudation Patterns Shape a Similar Microbial Community? – Pil Y – Journal of Botanical Sciences

Water and extremophile microbiome

Epiphytic bacterial communities of the alga Fucus vesiculosus in oil-contaminated water areas of the Barents Sea – D. V. Pugovkin – Doklady Biological Sciences

Warmer night-time temperature promotes microbial heterotrophic activity and modifies stream sediment community – Anna Freixa – Global Change Biology

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

Built environment

Inoculum composition determines microbial community and function in an anaerobic sequential batch reactor – Allison R. Perrotta – PLoS ONE

Bioinformatics

*Review: A review of bioinformatics tools for bio-prospecting from metagenomic sequence data – Despoina Deppie Roumpeka – Frontiers in Genetics

Techniques

Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity – Stanislav S. Terekhov – PNAS

Microbes in the news

From mice, clues to microbiome’s influence on metabolic disease – EurekaAlert

Bacteria Hysteria

Dog parks ground zero for deadly bacteria? How to keep your pet safe from leptospirosis – ABC15

February 17, 2017

Today the incoming is filled with some compelling reviews; considering periodontal inflammation and C.diff with IBD (separately), as well some biopesticide ethics discussion, and mention of exciting biome research mergers and funding afoot. Read on!

Human oral microbiome

Review: Contribution of proteomics to our understanding of periodontal inflammation– Nagihan Bostanci- Proteomics

Human vaginal microbiome

Subclinical alteration of the cervical–vaginal microbiome in women with idiopathic infertility-Giuseppina Campisciano- Journal of Cellular Physiology

Human gut microbiome

Review: Systematic review with meta-analysis: the impact of Clostridium difficile infection on the short and long-term risks of colectomy in inflammatory bowel disease– Law C- Alimentary Pharmacology and Therapeutics

Review: Therapeutic modulation of gut microbiota in inflammatory bowel disease: More questions to be answered– Yu Qi Qiao- Journal of Digestive Diseases

Fecal microbiota

Successful Resolution of Recurrent Clostridium difficile Infection using Freeze-Dried, Encapsulated Fecal Microbiota; Pragmatic Cohort Study– Christopher Staley- The American Journal of Gastroenterology

Plant, root, and soil microbiome

Effect of postharvest practices including degreening on citrus carpoplane microbial biomes– Gomba A.- Journal of Applied Microbiology

Biopesticides

Review: Should the biofilm mode of life be taken into consideration for microbial biocontrol agents?– Caroline Pandin- Microbial Biotechnology
http://onlinelibrary.wiley.com/doi/10.1111/1751-7915.12693/full

Microbes in the news

Laundry hygiene—how to get more than clean- Bockmuhl DP- Applied Microbiology

DNA Analysis Reveals Secret Microbiomes in Cities– Paula Solferini Rothman- BU News Service

Microbes on the market

Symbiotix Biotherapies Announces Issuance of First Composition of Matter Patent Covering a Microbiome-derived Therapeutic Molecule– Yahoo Finance

Vedanta Teams with Stanford and Leiden Universities for Microbiome Therapeutics– Genetic Engineering and Biotechnology News

Research Funding

U Of M Commercialization Grants Target Microbiome Test, Sleep Disorders, Epilepsy- Dan Jacobson– Twin Cities Business

February 17, 2017

Today the incoming research is rich in reviews, including one article examining periodontal inflammation and another examining  C.diff and IBD, also a biopesticide ethics discussion and some exciting funding and research mergers in the mix. Read on!

Human oral microbiome

Review: Contribution of proteomics to our understanding of periodontal inflammation– Nagihan Bostanci- Proteomics

Human vaginal microbiome

Subclinical alteration of the cervical–vaginal microbiome in women with idiopathic infertility-Giuseppina Campisciano- Journal of Cellular Physiology

Human gut microbiome

Review: Systematic review with meta-analysis: the impact of Clostridium difficile infection on the short and long-term risks of colectomy in inflammatory bowel disease– Law C- Alimentary Pharmacology and Therapeutics

Review: Therapeutic modulation of gut microbiota in inflammatory bowel disease: More questions to be answered– Yu Qi Qiao- Journal of Digestive Diseases

Fecal microbiota

Successful Resolution of Recurrent Clostridium difficile Infection using Freeze-Dried, Encapsulated Fecal Microbiota; Pragmatic Cohort Study– Christopher Staley- The American Journal of Gastroenterology

Plant, root, and soil microbiome

Effect of postharvest practices including degreening on citrus carpoplane microbial biomes– Gomba A.- Journal of Applied Microbiology

Biopesticides

Review: Should the biofilm mode of life be taken into consideration for microbial biocontrol agents?– Caroline Pandin- Microbial Biotechnology

Microbes in the news

Review: Laundry hygiene—how to get more than clean– Bockmuhl DP- Applied Microbiology

DNA Analysis Reveals Secret Microbiomes in Cities– Paula Solferini Rothman- BU News Service

Vedanta Teams with Stanford and Leiden Universities for Microbiome Therapeutics– Genetic Engineering and Biotechnology News

Microbes on the market

Symbiotix Biotherapies Announces Issuance of First Composition of Matter Patent Covering a Microbiome-derived Therapeutic Molecule- Yahoo Finance

Research Funding

U Of M Commercialization Grants Target Microbiome Test, Sleep Disorders, Epilepsy- Dan Jacobson– Twin Cities Business

February 16, 2017

Events and jobs

 Microbiology assistant or associate professor – Universidad de los Andes (Bogotá, Colombia)

PhD – Mechanisms of bacterial community dynamics in oral biofilms – The University of Sheffield, UK

General microbiome

Microbiome and Cardiac Health – Enrico Biffi – Integrative Cardiology

Editorial: Signals to sociality: how microbial communication fashions communities – Karine A. Gibbs – FEMS Microbiology Reviews

Pregnancy and early life

Assessment of complementary feeding of Canadian infants: effects on microbiome & oxidative stress, a randomized controlled trial – Wafaa Qasem – BMC Pediatrics

Human oral microbiome

Dysbiosis of oral buccal mucosa microbiota in patients with oral lichen planus – Yuan He – Oral Diseases

Integrated metagenomic data analysis demonstrates that a loss of diversity in oral microbiota is associated with periodontitis – Dongmei Ai – BMC Genomics 2017

Human respiratory microbiome

Bacterial Topography of the Healthy Human Lower Respiratory Tract – Robert P. Dickson – American Society for Microbiology (mBio)

Human vaginal microbiome

Distinct effects of the cervico-vaginal microbiota and herpes simplex type 2 infection on female genital tract immunology – Shannon B. – The Journal of Infectious Diseases

Human gut microbiome

DIFFERENCES IN GUT MICROBIOTA ACTIVITY (ANTIMICROBIALS, POTENTIAL MUTAGENS, AND STEROLS) ACCORDING TO DIET – P. OLEJNÍKOVÁ – Acta Alimentaria

Inediibacterium massiliense gen. nov., sp. nov., a new bacterial species isolated from the gut microbiota of a severely malnourished infant – Maryam Tidjani Alou – Antonie van Leeuwenhoek

Diversity and enterotype in gut bacterial community of adults in Taiwan – Chao Liang – BMC Genomics

Review: Meta-analysis of the human gut microbiome from urbanized and pre-agricultural populations – Leonardo Mancabelli – Environmental Microbiology

Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn’s disease in the Ryukyu Islands – Shigeki Nakagome – Human Genetics

Genomic Microdiversity of Bifidobacterium pseudocatenulatum Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention – Guojun Wu – American Socieity for Microbiology (mBio)

Review: Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases – Lieke WJ van den Elsen – Clinical and Translational Immunology

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Host Genotype and Gut Microbiome Modulate Insulin Secretion and Diet-Induced Metabolic Phenotypes – Julia H. Kreznar – Cell Reports

Melatonin prevents obesity through modulation of gut microbiota in mice – Pengfei Xu – Journal of Pineal Research

Inonotus obliquus polysaccharide regulates gut microbiota of chronic pancreatitis in mice – Yang Hu – AMB Express

Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet – Sophie Comtet-Marre – Frontiers in Microbiology

Animal microbiome

Succession and dynamics of Pristionchus nematodes and their microbiome during decomposition of Oryctes borbonicus on La Réunion Island – Jan M. Meyer – Environmental Microbiology

Plant, root, and soil microbiome

Effect of Elevated UV-B Radiation on Microbial Biomass C and Soil Respiration in Different Barley Cultivars Under Field Conditions – Yunsheng Lou – Water, Air, Soil Pollution

Comment: Isolation and screening of bacteria for their diazotrophic potential and their influence on growth promotion of Maize seedlings in greenhouses – Jeffrey S. Norman – Frontiers in Plant Science

Effects of Vegetation and Temperature on Nutrient Removal and Microbiology in Horizontal Subsurface Flow Constructed Wetlands for Treatment of Domestic Sewage – Qingwei Zhou – Water, Air, Soil Pollution

Editorial: Biotrophic Plant-Microbe Interactions – Pietro D. Spanu – Frontiers in Plant Science

Structural dynamics of microbial communities in polycyclic aromatic hydrocarbon-contaminated tropical estuarine sediments undergoing simulated aerobic biotreatment – Chioma C. Obi – Applied Microbiology and Biotechnology

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA – Kathleen H. Lavoie – PloS ONE

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

Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank – Marcio F. A. Leite – Scientific Reports

Syntrophobacteraceae-affiliated species are major propionate-degrading sulfate reducers in paddy soil – Pengfei Liu – Environmental Microbiology

Soil microbial community responses to contamination with silver, aluminium oxide and silicon dioxide nanoparticles – C. F. McGee – Ecotoxicology

Influence of straw incorporation with and without straw decomposer on soil bacterial community structure and function in a rice-wheat cropping system – Jun Zhao – Environmental biotechnology

Bacterial community shift and hydrocarbon transformation during bioremediation of short-term petroleum-contaminated soil – Manli Wu – Environmental Pollution

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Mineralizing Filamentous Bacteria from the Prony Bay Hydrothermal Field Give New Insights into the Functioning of Serpentinization-Based Subseafloor Ecosystems – Celine Pisapia – Frontiers in Microbiology

Food microbiology

Metagenomic Sequencing for Surveillance of Food- and Waterborne Viral Diseases – David F. Nieuwenhuijse – Frontiers in Microbiology

Masters Thesis: Effects of Cavitation on the Removal and Inactivation of Listeria and Salmonella from the Surface of Tomatoes and Cantaloupe – Joshua Jungho Lee – Virginia Tech

Chemical characterization of the glycated myofibrillar proteins from grass carp (Ctenopharyngodon idella) and their impacts on the human gut microbiota in vitro fermentation – Kaining Han – Food & Function

Spoilage of Microfiltered and Pasteurized Extended Shelf Life Milk Is Mainly Induced by Psychrotolerant Spore-Forming Bacteria that often Originate from Recontamination – Etienne V. Doll – Frontiers in Microbiology

Detection and Enumeration of Spore-Forming Bacteria in Powdered Dairy Products – Aoife J. McHugh – Frontiers in Microbiology

Probiotics / prebiotics

Probiotic roles of Lactobacillus sp. in swine: insights from gut microbiota – V.D.V. Valeriano – Journal of Applied Microbiology

Physiological Changes of Surface Membrane in Lactobacillus with Prebiotics – Mingfang Pan – Journal of Food Science

Bioinformatics

Comparative Analysis of Soil Microbiome Diversity using QIIME and CloVR Pipelines – Puniethaa Prabhu – Biometrics and Bioinformatics

A phylogenetic transform enhances analysis of compositional microbiota data – Justin D Silverman (Duke University) – eLife

MetaTopics: an integration tool to analyze microbial community profile by topic model – Jifang Yan – BMC Genomics 2017

Enhancing the clinical coverage and anticancer efficacy of immune checkpoint blockade through manipulation of the gut microbiota – Jonathon M. Pitt – OncoImmunology

Techniques         

Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research – Sebastian Menke – Frontiers in Microbiology

Microbes on the market 

Day Two link with Johnson & Johnson on personalized microbiome analysis for diabetes nutrition – Eliot Beer – nutraingredients.com

Microbes in the news

News Feature: Cleaning up the hygiene hypothesis – Megan Scudellari – PNAS

Ed’s non-microbiology picks

Decline in global oceanic oxygen content during the past five decades – Sunke Schmidtko – Nature

Tropical ancient DNA reveals relationships of the extinct Bahamian giant tortoise Chelonoidis alburyorumChristian Kehlmaier – Proceedings of the Royal Society (Biological Sciences)

Long-term trends in the honeybee ‘whooping signal’ revealed by automated detection – Michael Ramsey – PloS One

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

Bioinformatics

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

Techniques

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)