April 18, 2017

Today’s digest hosts a number of rhizosphere-related publications as well as a good amount of interesting microbiome-host-health science.  Coming up next week is BioData World West 2017, a conference focused on Genomics/Precision Medicine/AI that I will be attending – I’ll keep an eye out for anything microbiome-related!

Events and jobs

2017 Metagenomics Workshop – Edwards Lab Event (Bioinformatics)

BioData World West 2017 – Precision Medicine, AI, Genomics Conference

General microbiome

Biological Determinants of Health: Genes, Microbes, and Metabolism Exemplars of Nursing Science – Erin P. Ferranti – Nursing Outlook

* Microbiotal-Host Interactions and Hypertension – Sarah Galla – Physiology

Multi-site human microbiome

The Landscape Ecology and Microbiota of the Human Nose, Mouth, and Throat – Diana M. Proctor – Cell Host & Microbe

Human respiratory microbiome

* The microbiome in respiratory medicine: current challenges and future perspectives – Rosa Faner – European Respiratory Journal

Human skin microbiome

Living in Peace: Host-Microbiota Mutualism in the Skin – Daniel J. Campbell – Cell Host & Microbe

Human gut microbiome

The Gut Microbiome: Connecting Spatial Organization to Function – Carolina Tropini – Cell Host & Microbe

Lactobacillus casei DG and its postbiotic reduce the inflammatory mucosal response: an ex-vivo organ culture model of post-infectious irritable bowel syndrome – Compare D – BMC Gastroenterology

Animal experiments

Age-Associated Microbial Dysbiosis Promotes Intestinal Permeability, Systemic Inflammation, and Macrophage Dysfunction – Netusha Thevaranjan – Cell Host & Microbe

Animal microbiome

PrePrint – Succession of embryonic and intestinal bacterial communities of Atlantic salmon – Jep Lokesh – bioRxiv

The Role of Rumen Microbiome on Feed Efficiency of Grazing Cattle [page 138] – Leluo Guan – 28th Annual Florida Ruminant Nutrition Symposium

Structure and dynamics of the gut bacterial microbiota of the bark beetle, Dendroctonus rhizophagus (Curculionidae: Scolytinae) across their life stages – Carlos Iván Briones-Roblero – PLOS One

Plant, root, and soil microbiome

The role of soil chemistry and plant neighbourhoods in structuring fungal communities in three Panamanian rainforests – Tyler Schappe – Journal of Ecology

Host plant compatibility shapes the proteogenome of Frankia coriariae – Amir Ktari – Frontiers in Microbiology

Managing and manipulating the rhizosphere microbiome for plant health: A systems approach – Matthew D. Wallenstein – Rhizosphere

In vitro and In vivo biofilm formation by Azotobacter isolates and its relevance to rhizosphere colonization – Mohd. Musheer Altaf – Rhizosphere

Metabolism of pyrene through phthalic acid pathway by enriched bacterial consortium composed of Pseudomonas, Burkholderia, and Rhodococcus (PBR) – Sagar Vaidya – 3 Biotech

Effects of titanium dioxide nanoparticles on soil microbial communities and wheat biomass – Janine Moll – Soil Biology and Biochemistry

The effect of simulated warming on root dynamics and soil microbial community in an alpine meadow of the Qinghai-Tibet Plateau – Changting Wang – Applied Soil Ecology

Water and extremophile microbiome

Impacts of sea-level rise on sediment microbial community structure and function in two New England salt marshes, USA – Matt R. Simon – Journals of Soils and Sediments

A critical assessment of the microorganisms proposed to be important to enhanced biological phosphorus removal in full-scale wastewater treatment systems – Mikkel Stokholm-Bjerregaard – Frontiers in Microbiology

Applicability of cryoconite consortia of microorganisms and glacier-dwelling animals in astrobiological studies – Krzysztof Zawierucha – Contemporary Trends in Geoscience

Built environment

Review – Microbiological diagnosis of device-related biofilm infections – Yijuan Xu – APMIS

Patent Application – MONITORING AND MANAGING A FACILITY MICROBIOME – Dillon, Harrison – Free Patents Online

Microbes in space

Origins of Life on Mars: NASA’s Rovers Were Never Sterilized – Rhawn Gabriel Joseph – Cosmology.com

Phages and viruses

Mini Review Article – Phages in the Human Body – Ferran Navarro – Frontiers in Microbiology

Bioinformatics

* A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes – Wontack Han – Research in Computational Molecular Biology. RECOMB 2017.

Techniques

Effect of environmental variation on estimating the bacterial species richness – Jongjian Chen – Frontiers in Microbiology

Thesis – USE OF MOLECULAR METHODS IN BIOTHREAT PREPAREDNESS – Katja Koskela – National Defense University: Research Publications No. 13

Microbes in the news

Pets During Pregnancy Trigger Gut Bacteria Changes for Infants That May Cut Obesity Risk, Study Finds

Gut microbiome dysregulation implicated in OCD

Microbes on the market

Innovative Microbiome-based IBD Therapeutics to Be Developed Under New Partnership

Microbiome drug candidate prevents recurrence of C. difficile infection

Ed’s non-microbiology picks

Climate change causes glacial river in Yukon to change direction

Self-taught artificial intelligence beats doctors at predicting heart attacks

Stroke rates appear to be rising steadily in young adults

Costs of Selective Attention: When Children Notice What Adults Miss – Daniel J. Plebanek – APS

California Dryness and Recovery Challenge Multi-Century Odds

March 29, 2017

Today’s digest is chock-full of human gut studies related to disease, soil/plant and water/environmental studies, quite a lot of research on animal microbiomes and symbiotic microbes, as well as some discussion of techniques to improve various metagenomic applications.

Events and jobs

Scientist – Microbiology Development – BD (Becton, Dickinson and Company)

Microbiology Technical Manager – UKAS – W.Midlands

Multi-site human microbiome

Integration of microbiome and epigenome to decipher the pathogenesis of autoimmune diseases – Beidi Chen – Journal of Autoimmunity

Human respiratory microbiome

Integrating the microbiota of the respiratory tract with the unified airway model – Alissa S. Hanshew – Respiratory Medicine

The role of acute and chronic respiratory colonization and infections in the pathogenesis of COPD – Janice M. Leung – Respirology

Human nearly-sterile sites (blood, organs, brain)

* The blood DNA virome in 8,000 humans – Ahmed Moustafa – PLOS Pathogens

Human gut microbiome

Role of External and Environmental Factors in Drug Resistance Emergence: Gut Microbiota – Daniel Ryan – Drug Resistance in Bacteria, Fungi, Malaria, and Cancer

* Changes in intestinal microbiota composition and metabolism coincide with increased intestinal permeability in young adults under prolonged physiologic stress – J. Philip Karl – American Journal of Physiology-Gastrointestinal and Liver Physiology

Robust Microbiota-Based Diagnostics for Inflammatory Bowel Disease – A. Eck – Journal of Clinical Microbiology

Tackling the Antibiotic Resistance: The “Gut” Feeling – Richa Misra – Drug Resistance in Bacteria, Fungi, Malaria, and Cancer

Book Chapter – Human Gut Microbiota and Obesity During Development – Tomás Cerdó – Adiposity – Omics and Molecular Understanding

Fecal microbiota transplantation – methods of treatment of recurrent Clostridium difficile infections and other diseases – Juszczuk K – Postepy Hig Med Dosw (Online)

Gut Colonization by Methanogenic Archaea Is Associated with Organic Dairy Consumption in Children – van de Pol JA – Frontiers in Microbiology

Gut Microbiome in Chronic Kidney Disease – R. G. Armani – Current Hypertension Reports

Sex-dependent effects on gut microbiota regulate hepatic carcinogenic outcomes – Guoxiang Xie – Scientific Reports

Gut microbiome analysis of type 2 diabetic patients from the Chinese minority ethnic groups the Uygurs and Kazaks – Ye Wang – PLOS ONE

Animal experiments 

Stressor exposure has prolonged effects on colonic microbial community structure in Citrobacter rodentium-challenged mice – Jeffrey D. Galley – Scientific Reports

Engineered Resistant-Starch (ERS) Diet Shapes Colon Microbiota Profile in Parallel with the Retardation of Tumor Growth in In Vitro and In Vivo Pancreatic Cancer Models – Concetta Panebianco – Nutrients

Alcohol-related changes in the intestinal microbiome influence neutrophil infiltration, inflammation and steatosis in early alcoholic hepatitis in mice – Patrick P. Lowe  – PLOS ONE

Altered gut microbiome in a mouse model of Gulf War Illness causes neuroinflammation and intestinal injury via leaky gut and TLR4 activation – Firas Alhasson – PLOS ONE

Olive oil bioactives protect pigs against experimentally-induced chronic inflammation independently of alterations in gut microbiota – Martin Liehr – PLOS ONE

Animal microbiome

Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus – Eva Novakova – Frontiers in Microbiology

The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot – Devin B. Holman – BMC Microbiology

Fungal diversity and community structure in gut, mound and surrounding soil of fungus-cultivating termites – Huxley Mae Makonde – African Journal of Microbiology Research

Integrated metabolism in sponge–microbe symbiosis revealed by genome-centered metatranscriptomics – Lucas Moitinho-Silva – The ISME Journal (Microbial Ecology)

Inferring Microbial Interactions in the Gut of the Hong Kong Whipping Frog (Polypedates megacephalus) and a Validation Using Probiotics – Francis C. Weng – Frontiers in Microbiology

Plant, root, and soil microbiome

Mineral Ecology: Surface Specific Colonization and Geochemical Drivers of Biofilm Accumulation, Composition, and Phylogeny – Aaron A. Jones – Frontiers in Microbiology

Defining the core citrus leaf- and root-associated microbiota: Factors associated with community structure and implications for managing Huanglongbing (Citrus greening) disease – Ryan A. Blaustein – American Society for Microbiology

The preservation of microbial DNA in archived soils of various genetic types – Ekaterina A. Ivanova – PLOS ONE

Unknown risks to soil biodiversity from commercial fungal inoculants – Miranda M. Hart – Nature Ecology and Evolution

Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils – Li-Li Han – Scientific Reports

Relationship of microbial communities and suppressiveness of Trichoderma fortified composts for pepper seedlings infected by Phytophthora nicotianae – Margarita Ros – PLOS ONE

Metagenomic analyses of bacterial endophytes associated with the phyllosphere of a Bt maize cultivar and its isogenic parental line from South Africa – Ramadimetja A – World Journal of Microbiology and Biotechnology

Water and extremophile microbiome

* Characterization of culturable bacteria isolated from hot springs for plant growth promoting traits and effect on tomato (Lycopersicon esculentum) seedling – Kinjal Samir Patel – Comptes Rendus Biologies

* Microbial indicators as a diagnostic tool for assessing water quality and climate stress in coral reef ecosystems – Bettina Glasl – Marine Biology

Pre-print – Response Of Microbial Community Function To Fluctuating Geochemical Conditions Within A Legacy Radioactive Waste Trench Environment – Xabier Vázquez-Campos – bioRxiv

* Patterns of variation in diversity of the Mississippi river microbiome over 1,300 kilometers – Jason T. Payne – PLOS ONE

Food microbiology

Monitoring of the bacterial communities of bamboo shoots (Dendrocalamus latiflorus) during pickling process – Xuejuan Xia – International Journal of Food Science + Technology

Bioinformatics

Preprint – MIMIX: a Bayesian Mixed-Effects Model for Microbiome Data from Designed Experiments – Neal S. Grantham – arXiv

Techniques

Integrated Methodology to Characterize Microbial Populations and Functions across Small Spatial Scales in an Oil Production Facility – Christopher R. Marks – Routledge

Next-Generation Sequencing Combined with Specific PCR Assays To Determine the Bacterial 16S rRNA Gene Profiles of Middle Ear Fluid Collected from Children with Acute Otitis Media – Saara Sillanpää – American Society for Microbiology Journals

Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding – Matthieu Leray – PeerJ

Novel 16S rDNA primers revealed the diversity and habitats-related community structure of sphingomonads in 10 different niches – Yili Huang – Antonie van Leeuwenhoek

Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications – Ahsanuddin S – Journal of Biomolecular Techniques

Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches – Sepideh Lamei – PLOS ONE

Microbes in the news 

Bacteria, deadwood and climate change—forest floor as carbon sink

Basic microbiology research study unexpectedly uncovers practical findings for growers

Bacteria That Cause Human Diseases Found in Orca Blowholes

Bacteria Hysteria

Keep Your Phone Bacteria Free with PhoneSoap

Science, publishing, and career 

Behar, Finberg and Luzuriaga elected fellows of American Academy of Microbiology

Ed’s non-microbiology picks 

Spinach Leaf Transformed Into Beating Human Heart Tissue

Low Socioeconomic Status Affects Life Expectancy More Than Obesity

Caesarean sections and for-profit status of hospitals: systematic review and meta-analysis – Ilir Hoxha – BMJ Open

Work organization and mental health problems in PhD students – Katia Levecque – Research Policy

Influence of Anthropogenic Climate Change on Planetary Wave Resonance and Extreme Weather Events – Michael E. Mann – Scientific Reports

March 15, 2017

Today’s digest is full of environmental, soil/plant/root, and water related studies among a few gut microbiome studies and some opinion pieces.

Events and jobs

Event: Gut Feeling – How bacteria influence our wellbeing – EMBL-EBI – 21-May-2017

Event: Meeting of the Microbiome Minds – Colorado State University

General microbiome

Opinion: The study of microbiota needs both microbiologists and medical doctors – Didier Raoult – CMI

Pregnancy and early life

Review: Distinct Roles of Cervical Epithelia and Stroma in Pregnancy and Parturition – Shanmugasundaram Nallasamy – Seminars in Reproductive Medicine (Thieme)

The shape of the microbiome in early life – Erika von Mutius – Nature Medicine

Multi-site human microbiome

Examination of Host Phenotypes in Gambusia affinis Following Antibiotic Treatment – Jeanette M. Carlson – J. Vis. Exp.

Human respiratory microbiome

Strong incidence of Pseudomonas aeruginosa on bacterial rrs and ITS genetic structures of cystic fibrosis sputa – Laurence Pages-Monteiro – PLOS One

Human skin microbiome

Review: Cutaneous wound biofilm and the potential for electrical stimulation in management of the microbiome – Mohammed Ashrafi – Future Microbiology

Human vaginal microbiome

Vaginal Microbiome and Its Relationship to Behavior, Sexual Health, an Sexually Transmitted Diseases – Felicia M. Lewis – Obstetrics & Gynecology

Women view key sexual behaviours as the trigger for the onset and recurrence of bacterial vaginosis – Jade E. Bilardi – PLOS One

Human oral microbiome

Clustering of Subgingival Microbiota Reveals Microbial Disease Ecotypes Associated with Clinical Stages of Periodontitis in a Cross-Sectional Study – Sebastien Boutin – Frontiers in Microbiology

Human gut microbiome

*The altered gut microbiota in adults with cystic fibrosis – D.G. Burke – BMC Microbiology

Consumption of a diet rich in Brassica vegetables is associated with a reduced abundance of sulphate-reducing bacteria: a randomised crossover study – Lee Kellingray – Molecular Nutrition & Food Research

Gastric Acid Suppression Is Associated with an Increased Risk of Adverse Outcomes in Inflammatory Bowel Disease – Shah R – Digestion

NLRP12 attenuates colon inflammation by maintaining colonic microbial diversity and promoting protective commensal bacterial growth – Liang Chen – Nature Immunology

Gut microbiome diversity and high fibre intake are related to lower long term weight gain – Menni C – International Journal of Obesity

We are not alone: a case for the human microbiome in extra intestinal diseases – S. Shivaji – Gut Pathogens

The intestinal microenvironment in sepsis – Katherine T Fay – BBA – Molecular Basis of Disease

The Gut Microbiome and Its Role in Cardiovascular Diseases – W. H. Wilson Tang – Circulation

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

Mechanisms and effects of arsanilic acid on antibiotic resistance genes and microbial communities during pig manure digestion – Wei Sun – Bioresource Technology

Dietary Broccoli Alters Rat Cecal Microbiota to Improve Glucoraphanin Hydrolysis to Bioactive Isothiocyanates – Xiaoji Liu – Nutrients

Sorghum and wheat differentially affect caecal microbiota and associated performance characteristics of meat chickens – Eduardo Crisol-Martinez – PeerJ

Microbiome and metabolome modifying effects of several cardiovascular disease interventions in apo-E−/− mice – Paul M. Ryan – Microbiome

Infection with diverse immune-modulating poxviruses elicits different compositional shifts in the mouse gut microbiome – Daniel Aguirre de Cárcer – PLOS One

Animal microbiome (for animals in the wild)

Diverse bacterial communities exist on canine skin and are impacted by cohabitation and time – Sheila Torres – PeerJ

Fine Flounder (Paralichthys adspersus) Microbiome Showed Important Differences between Wild and Reared Specimens – Carolina Ramirez – Frontiers in Microbiology

Use of signature-tagged mutagenesis to identify genes associated with colonization of sheep by E. coli O157:H7 – Nancy A. Cornick – Veterinary Microbiology

The oral microbiota of domestic cats harbors a wide variety of Staphylococcus species with zoonotic potential – Ciro Cesar Rossi – Veterinary Microbiology

The bovine paranasal sinuses: Bacterial flora, epithelial expression of nitric oxide and potential role in the in-herd persistence of respiratory disease pathogens – Gerard M. Murray – PLOS One

Plant, root, and soil microbiome

Analysis of microbiota involved in the aged natural fermentation of indigo – Takahiro Okamoto – World Journal of Microbiology and Biotechnology

Microbial solvent formation revisited by comparative genome analysis – Anja Poehlein – Biotechnology for Biofuels

Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities – Wepking, C – Proceedings of the Royal Society B-Biological Science

Legal immigrants: invasion of alien microbial communities during winter occurring desert dust storms – Tobias Weil – Microbiome

Characterization of microbial communities during start-up of integrated fixed-film activated sludge (IFAS) systems for the treatment of oil sands process-affected water (OSPW) – Chunkai Huang – Biochemical Engineering Journal

Effects of experimental addition of nitrogen and phosphorus on microbial and metazoan communities in a peatbog – Tomasz Mieczan – European Journal of Protistology

The potential of native species as bioenergy crops on trace-element contaminated Mediterranean lands – Dominquez MT – Sci Total Environment

Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar – Jaiswal AK – Scientific Reports

Growth and 137Cs uptake and accumulation among 56 Japanese cultivars of Brassica rapa, Brassica juncea and Brassica napus grown in a contaminated field in Fukushima: Effect of inoculation with a Bacillus pumilus strain – Salem Djedidi – Journal of Environmental Radioactivity

Antibiotic mixture effects on growth of the leaf-shredding stream detritivore Gammarus fossarum – Mirco Bundschuh – Ecotoxicology

Microbial community changes during different empty bed residence times and operational fluctuations in an air diffusion reactor for odor abatement – Elisa Rodriguez – Science of the Total Environment

Response of indigenously developed bacterial consortia in progressive degradation of polyvinyl chloride – Mohammad S Anwar – Protoplasma

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

Conference: Effects of simulated deep-sea mining impacts on microbial communities and functions in the DISCOL experimental area – Vonnahme, T – EU FP7 MIDAS final meeting,

Effects of residual organics in municipal wastewater on hydrogenotrophic denitrifying microbial communities – Wei Xing – Journal of Environmental Sciences

PrePrint: Plasmid DNA analysis of pristine groundwater microbial communities reveal extensive2 presence of metal resistance genes – Ankita Kothari – bioRxiv

Climate, soil and plant functional types as drivers of global fine-root trait variation – Gregoire T. Freschet – Journal of Ecology

Winter ecology of a subalpine grassland: Effects of snow removal on soil respiration, microbial structure and function – Konstantin Gavazov – Science of the Total Environment

Deterministic influences exceed dispersal effects on hydrologically-connected microbiomes – Emily B. Graham – Environmental Microbiology

Review: Microbiome involved in microbial electrochemical systems (MESs): A review – Saratale RG – Chemosphere

Chapter Four – Polar Marine Microorganisms and Climate Change – C. Verde – Advances in Microbial Physiology

The patterns of bacterial community and relationships between sulfate-reducing bacteria and hydrochemistry in sulfate-polluted groundwater of Baogang rare earth tailings – Xinli An – Environmental Science and Pollution Research

Characterization of bacterial community associated with phytoplankton bloom in a eutrophic lake in South Norway using 16S rRNA gene amplicon sequence analysis – Niranjan Nitin Parulekar – PLOS One

Food microbiology

Editorial: Inner Workings: Fermented foods offer up a versatile microbial model system – Alla Katsnelson – PNAS

Probiotics / prebiotics

News article: IBS cure? Probiotics could REDUCE irritable bowel syndrome symptoms AND stress – Olivia Lerche – express.co.uk

 Bioinformatics

Applied Metagenomics for Biofuel Development and Environmental Sustainability – Antonio Djalma Nunes Ferraz Junior – Advances of Basic Science for Second Generation Bioethanol from Sugarcane

DEMOGRAPHICS INDUCE EXTINCTION OF DISEASE IN AN SIS MODEL BASED ON CONDITIONAL MARKOV CHAIN – XIAOFENG LUO – Journal of Biological Systems

Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters – Yu Shang – PLOS One

Techniques

Comparative analysis of microbial communities during enrichment and isolation of DDT-degrading bacteria by culture-dependent and -independent methods – Beibei Wang – Science of The Total Environment

*How to know the fungi: combining field inventories and DNA-barcoding to document fungal diversity – Camille Truong – New Phytologist

Sampling Strategies for Three-Dimensional Spatial Community Structures in IBD Microbiota Research – Shaocun Zhang – Frontiers in Cellular and Infection Microbiology

Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions – John J. Schellenberg – Journal of Microbiological Methods

Ed’s non-microbiology picks (news articles)

First Time Ever: Gene Therapy Reverses Sickle Cell Disease

Earth’s oceans are warming 13% faster than thought, and accelerating

MIT researchers create new form of matter

Gene therapy treats muscle-wasting disease in dogs

World’s oldest plant fossil discovered by student pushes evolution of complex life back 400 million years

 

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