Category Archives: Metagenomics & Bioinformatics

February 17, 2017

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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

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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 alburyorum – Christian 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 9, 2017

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Metabolomic analysis to determine affects of antibiotic treatment on the microbiome, capsular polysaccharide structure from marine bacterium, altering soil bacterial communities from use of organic-inorganic fertilization, new CRISPR-Cas systems discovered in uncultivated microbes.

General microbiome

Metabolic effects of Lactobacillus reuteri DSM 17938 in people with type 2 diabetes: A randomized controlled trial – Reza Mobini – Diabetes, Obesity and Metabolism

Pregnancy and early life

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

Human oral microbiome

Isolation and identification methods of Rothia species in oral cavities – Osamu Tsuzukibashi – Journal of Microbiological Methods

Association of oral microbiome with type 2 diabetes risk – J Long – Journal of Periodontal Research

Human skin microbiome

Microbiome precision editing: Using PEG as a selective fermentation initiator against methicillin-resistant Staphylococcus aureus – Ming-Shan Kao – Biotechnology Journal

Human gut microbiome

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

Rett Syndrome: A Focus on Gut Microbiota – Elisa Borghi – International Journal of Molecular Sciences

Colonization with enterotoxigenic Bacteroides fragilis is associated with early-stage colorectal neoplasia – Rachel V Purcell – PLOS ONE

Gut dysbiosis is associated with metabolism and systemic inflammation in patients with ischemic stroke – Kazuo Yamashiro – PLOS ONE

Glycomacropeptide sustains microbiota diversity and promotes specific taxa in an artificial colon model of elderly gut microbiota – Alexandra Ntemiri – Journal of Agricultural and Food Chemistry

Animal experiments

* Early life antibiotic exposure affects pancreatic islet development and metabolic regulation – Jiaying Li – Scientific Reports

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

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

Fish Intestinal Microbiome: Diversity and Symbiosis Unraveled by Metagenomics – AM Tarnecki – Journal of Applied Microbiology

Plant, root, and soil microbiome

Exploring the symbiont diversity of ancient western redcedars: arbuscular mycorrhizal fungi of long-lived hosts – Monika A Gorzelak – Molecular Ecology

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

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

Bacterial Community Structure after Long-term Organic and Inorganic Fertilization Reveals Important Associations between Soil Nutrients and Specific Taxa Involved in Nutrient Transformations – Fang Li – Frontiers in Microbiology

The effects of fluoride based fire-fighting foams on soil microbiota activity and plant growth during natural attenuation of perfluorinated compounds – Renato Nallin Montagnolli – Environmental Toxicology and Pharmacology

Chapter: Phytostimulation and Biocontrol by the Plant-Associated Bacillus amyloliquefaciens FZB42: An Update – Rainer Borriss – Bacilli and Agrobiotechnology

Chapter: New Insights in Plant-Associated Paenibacillus Species: Biocontrol and Plant Growth-Promoting Activity – Sadhana Lal – Bacilli and Agrobiotechnology

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones – Sihang Yang – Frontiers in Microbiology

Water and extremophile microbiome

The effects of elevated seawater temperatures on Caribbean gorgonian corals and their algal symbionts, Symbiodinium spp. – Tamar L. Goulet – PLOS ONE

* Structural characterization of an all-aminosugar-containing capsular polysaccharide from Colwellia psychrerythraea 34H – Angela Casillo – Antonie van Leeuwenhoek

Illumina sequencing-based analysis of sediment bacteria community in different trophic status freshwater lakes – Yu Wan – Microbiology Open

Bacterial communities in sediment of a Mediterranean Marine Protected Area – Valentina Catania – Canadian Journal of Microbiology

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

The effect of top-predator presence and phenotype on aquatic microbial communities – Karen E. Sullam – Ecology and Evolution

Metabolomics

Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions – Jocelyn M. Choo – mSphere

Techniques

A novel LCMSMS method for quantitative measurement of short-chain fatty acids in human stool derivatized with 12C- and 13C-labelled aniline – James Chun Yip Chan – Journal of Pharmaceutical and Biomedical Analysis

More microbes

* New CRISPR–Cas systems from uncultivated microbes – David Burstein – Nature

Adaptation of genetically monomorphic bacteria: evolution of copper resistance through multiple horizontal gene transfers of complex and versatile mobile genetic elements – D Richard – Molecular Ecology

Microbes in the news

Microbial Molecules from the Multitudes within Us – Matthew R. Redondo – Cell Metabolism

Boston Children’s Hospital and uBiome to Investigate Premature Births – PRWeb

Cholera bacteria stab and poison enemies at predictable rates – Georgia Institute of Technology – ScienceDaily

ADA funds Kostic Lab to create model linking the microbiome to type 1 diabetes – EurekAlert

February 8, 2017

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A dense Digest today, a lot of reviews on the human gut microbiome, a plethora of papers on plant, soil and water microbiomes, and an alarmingly high rate of multi-drug resistant bacteria from human fecal samples in China

Jobs

Teaching and Learning Fellow in Microbiome Data Analysis – University of British Columbia

Microbiology Quality Technician II – CR Bard

Postdoctoral Research Assistant on the Social Dimensions of the Microbiome – University of Oxford

General microbiology

Transcriptional characterization of Vibrio fischeri during colonization of juvenile Euprymna scolopes – Luke R. Thompson – Environmental Microbiology

Effect of antibiotics on bacterial populations: a multi-hierachical selection process – José Luis Martínez – F1000 Research

Plant growth promoting potential and phylogenetic characteristics of a lichenized nitrogen fixing bacterium, Enterobacter cloacae – Chidanandamurthy Thippeswamy Swamy – Journal of Basic Microbiology

*High rates of human faecal carriage of mcr-1-positive multi-drug resistant isolates emerge in China in association with successful plasmid families – Lan-Lan Zhong – bioRxiv

Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States – Yi Chen – PLoS One

Human skin microbiome

Significant disparities in allergy prevalence and microbiota between the young people in Finnish and Russian Karelia – Lasse Ruokolainen – Clinical & Experimental Allergy

Beyond Cell Division: the Ecological Roles of Autolysins in Oral Biofilm Communities – Nyssa Cullin – Current Oral Health Reports

Human lung microbiome

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

Human gut microbiome

Review: Intestinal Microbiota: Facts and Fiction – M Kverka – Digestive Diseases

Review: Evolutionary and ecological forces that shape the bacterial communities of the human gut – J S Messer – Mucosal Immunology

Review: Dietary Fiber and Prebiotics and the Gastrointestinal Microbiota – Hannah D. Holscher – Gut Microbes

Review: The Fungal Mycobiome and Its Interaction with Gut Bacteria in the Host – Qi Hui Sam – International Journal of Molecular Sciences

Review: The Gut Microbiome in Irritable Bowel Syndrome and Other Functional Bowel Disorders – Yehuda Ringel – Gastroenterology Clinics of North America

Many more human gut microbiome reviews available from the March Issue of the Gastroenterology Clinics of North America

Human gut-microbiome-brain axis

Editorial: Tightening the Case for Gut Microbiota in Autism-Spectrum Disorder – Jonathan Braun – CMGH Cellular and Molecular Gastroenterology and Hepatology

Review: The Microbiome-Gut-Brain Axis in Health and Disease – Timothy G. Dinan – Gastroenterology Clinics of North America

Metabolomics

Review: Mixing omics: combining genetics and metabolomics to study rheumatic diseases – Cristina Menni – Nature Reviews Rheumatology

Review: Emerging Approaches to Tuberculosis Drug Development: At Home in the Metabolome – Robert S. Jansen – Trends in Pharmacological Sciences

Rats Urinary Metabolome Reveals for the Potential Role of Functional Foods and Exercise in Obesity Management – Mohammed Farag – Food and Function

Untargeted metabolomics approach for unraveling robust biomarkers of nutritional status in fasted gilthead sea bream (Sparus aurata) – Ruben Gil-Solsona – PeerJ

Animal experiments

Mouse: Sex-Specific Effects of Organophosphate Diazinon on the Gut Microbiome and Its Metabolic Functions – Bei Gao – Environmental Health Perspectives

Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet – Hyunmin Koo – Journal of Microbiological Methods

Commentary: Zebrafish screens for new colitis treatments – a bottom-up approach – Jou A. Lee – The FEBS Journal

Mouse: Resistant starch can improve insulin sensitivity independently of the gut microbiota – Laure B. Bindels – Microbiome

Animal microbiome

Invited review: Large-scale indirect measurements for enteric methane emissions in dairy cattle: A review of proxies and their potential for use in management and breeding decisions – E. Negussie – Journal of Dairy Science

Variation of the microbiota and metabolome along the canine gastrointestinal tract – Julia B. Honneffer – Metabolomics

Effects of Organic Amendments on Microbiota Associated with the Culex nigripalpus Mosquito Vector of the Saint Louis Encephalitis and West Nile Viruses – Dagne Duguma – mSphere

Review: Progress in fish gastrointestinal microbiota research – An R. Wang – Reviews in Aquaculture

Diversity and functions of the sheep faecal microbiota: a multi-omic characterization – Alessandro Tanca – Microbial Biotechnology

Microbial shifts in the porcine distal gut in response to diets supplemented with Enterococcus Faecalis as alternatives to antibiotics – Pinghua Li – Scientific Reports

Plant, root and soil microbiome

Fungi from Brazilian Savannah and Atlantic rainforest show high antibacterial and antifungal activity – Paula de Paula Menezes Barbosa – Biocatalysis and Agricultural Biotechnology

Impact of Elevated CO2 and/or Temperature on the AM Fungal Diversity in Groundnut Rhizosphere under Open Top Chamber facility – HN Asha – International Journal of Current Microbiology and Applied Sciences

Seed-coating fenugreek with Burkholderia rhizobacteria enhances yield in field trials and can combat Fusarium wilt – Harish Kuma – Rhizosphere

Changes at the Rhizosphere Microbiota of the Sunflower–Orobanche cumana Wallr Pathosystem – TH Hristev – International Journal of Current Microbiology and Applied Sciences

Review: Phosphate Solubilizing Microbes: An Overview – KP Ingle – International Journal of Current Microbiology and Applied Sciences

Draft Genome Sequence of Plant Growth-Promoting Drought-Tolerant Bacillus sp. Strain CMAA 1363 Isolated from the Brazilian Caatinga Biome – Vanessa Nessner Kavamura – Genome Announcements

Effects of Garlic/Cucumber Relay Intercropping on Soil Enzyme Activities and the Microbial Environment in Continuous Cropping – Lantian Du – HortScience

Characterization of bacterial communities from Masseiras, a unique Portuguese greenhouse agricultural system – Cristina Becerra-Castro – Antonie van Leeuwenhoek

Soil microbial community responses to long-term land use intensification in subtropical grazing lands – Sutie Xu – Geoderma

The impact of salinity on the microbial response to drying and rewetting in soil – Kristin M. Rath

The influence of different concentrations of bio-organic fertilizer on cucumber Fusarium wilt and soil microflora alterations – Nan Huang – PLoS One

Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype – Jakson Leite – Frontiers in Plant Science

Microbial Interactions in the Phyllosphere Increase Plant Performance under Herbivore Biotic Stress – Muhammad Saleem – Frontiers in Microbiology

Water and extremophile microbiome

Complete Genome Sequence of Thermus thermophilus TMY, Isolated from a Geothermal Power Plant – Yasuhiro Fujino – Genome Announcements

Marine Microbes as a Potential Source of Cellulolytic Enzymes – N. Trivedi – Chapter 2 of Advances in Food and Nutrition Research, Vol. 79

Genetic toolbox for controlled expression of functional proteins in Geobacillus spp. – Ivan Pogrebnyakov – PLoS One

Coupled Effects of Electrical Stimulation and Antibiotics on Microbial Community in Three-Dimensional Biofilm-Electrode Reactors – Hai-Liang Song – Water, Air, & Soil Pollution

Do biofilm communities respond to the chemical signatures of fracking? A test involving streams in North-central Arkansas – Wilson H. Johnson – BMC Microbiology

Effects of chemical cleaning on RO membrane inorganic, organic and microbial foulant removal in a full-scale plant for municipal wastewater reclamation – Tong Yu – Water Research

Microbial nitrification, denitrification and respiration in the leached cinnamon soil of the upper basin of Miyun Reservoir – Wen Xu – Scientific Reports

Microbes in space

The Effects of HZE Particles, γ and X-ray Radiation on the Survival and Genetic Integrity of Halobacterium salinarum NRC-1, Halococcus hamelinensis, and Halococcus morrhuae – Leuko Stefan – Astrobiology

Survival, DNA Integrity, and Ultrastructural Damage in Antarctic Cryptoendolithic Eukaryotic Microorganisms Exposed to Ionizing Radiation – Pacelli Claudia – Astrobiology

Phages and viruses

Genomic sequence of ‘Candidatus Liberibacter solanacearum’ haplotype C and its comparison with haplotype A and B genomes – Jinhui Wang – PLoS One

Technology

Microbial Typing by Machine Learned DNA Melt Signatures – Nadya Andini – Scientific Reports

Bioinformatics

From Culture to High-Throughput Sequencing and Beyond: A Layperson’s Guide to the “Omics” and Diagnostic Potential of the Microbiome – Paul W. O’Toole – Gastroenterology Clinics of North America

Microbes in the news

2017 sneak peek: What the new year holds for science – Elizabeth Gibney – Nature

Is It the “Terrible Twos”? Or Is It a Disrupted Gut Microbiome? – Chris Kresser

Microbes on the market

Human Microbiome Market : Global Market Snapshot by 2020 – Persistence Market Research

February 3, 2017

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A review of microbes and cancer, seminal microbiome diversity, personalised microbiome-based approaches to Metabolic Syndrome, Thyrve: a new service offering testing and probiotic delivery, and Johnson & Johnson invests in Caelus.

Jobs

Microbiology Technologist Junior– Leeds

General microbiome

Review: Microbes and Cancer – Amiran Dzutsev- Annual Review of Immunology

Pregnancy and early life

Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling- Francesco Asnicar- mSystems

Associations between changes in the maternal gut microbiome and differentially methylated regions of diabetes-associated genes in fetuses: A pilot study from a birth cohort study-Kaori Tachibana- Journal of Diabetes Investigation

Human respiratory microbiome

Changes in the respiratory microbiome during acute exacerbations of idiopathic pulmonary fibrosis-Philip L. Molyneaux-Respiratory Research

Host genetic variation in mucosal immunity pathways influences the upper airway microbiome-Catherine Igartua- Microbiome

Human seminal microbiome

Seminal microbiome in men with and without prostatitis– Reet M€andar- International Journal of Urology

Blood microbiome

Blood Microbiome Quantity and the Hyperdynamic Circulation in Decompensated Cirrhotic Patients– Daniela Traykova- PLOS one

Human gut microbiome

Fecal Microbiota Transplantation in Inflammatory Bowel Disease– W.Reinisch- Digestive Diseases

Review: Role of gut microbiome in ankylosing spondylitis: an analysis of studies in literature– Yong-Yue Xu- Discovery Medicine

Feedback control of AHR signalling regulates intestinal immunity-Chris Schiering- Nature

Editorial: Commensal microbiota as a potential trigger of autoimmune uveitis-Reiko Horai- Expert Review of Clinical Immunology

Colonization with Helicobacter is concomitant with modified gut microbiota and drastic failure of the immune control of Mycobacterium tuberculosis-L. Majlessi- Mucosal Immunology

Review: Food matters: how the microbiome and gut–brain interaction might impact the development and course of anorexia nervosa– Beate Herpertz-Dahlmann- European Child & Adolescent Psychiatry

Gut microbiota dysbiosis contributes to the development of hypertension-Jing Li-Microbiome

Personalized microbiome-based approaches to metabolic syndrome management and prevention-Hagit Shapiro-Journal of Diabetes

Plant microbiome

Leaf-litter microbial communities in boreal streams linked to forest and wetland sources of dissolved organic carbon– Caroline E. Emilson-Ecosphere

Water microbiome

Sediment Microbial Diversity of Three Deep-Sea Hydrothermal Vents Southwest of the Azores-Teresa Cerqueira- Microbial Ecology

Bioinformatics

Consistent metagenomic biomarker detection via robust PCA-Mustafa Alshawaqfeh- Biology Direct

Microbes in the news

University of Maryland Students Send Bacteria to Space

VA is studying gut bacteria in PTSD, TBI patients following success in mice

Pores found in ‘platypus of microbiology’ bacterium push boundaries of evolution

What’s Your Gut Wellness Score? Thryve Launches With New Microbiome Testing Service for Better Health Through Your Stomach

Microbes on the market 

J&J invests in Caelus, pens pacts to grow microbiome R&D

Profound Improvements in Autistic Symptoms with Microbial Therapy

January 27, 2016

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Reviews on prenatal bacterial microbiota, mycobiome in the lower respiratory tract and interesting articles on association of HPV infection with vaginal microbiota; prebiotic and bioactive milk fraction improving NREM sleep.

General microbiome

Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data – Kelly M. Robinson – Microbiome

Pregnancy and early life

*Review: Does a prenatal bacterial microbiota exist? – M Hornef  -Mucosal Immunology

Human respiratory microbiome

*Review: Mycobiome in the Lower Respiratory Tract – A Clinical Perspective – Robert Krause- Frontiers in microbiology

Human vaginal microbiome

*Association of HPV infection and clearance with cervicovaginal immunology and the vaginal microbiota – B Shannon – Mucosal Immunology

Human gut microbiome

Review: Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle – Gina P. Rodriguez-Castaño – Frontiers in Genetics

Helicobacter pylori infection is associated with an altered gastric microbiota in children – K M Brawner – Mucosal Immunology

*Colonic Absorption of Low-Molecular-Weight Metabolites Influenced by the Intestinal Microbiome: A Pilot Study – Mitsuharu Matsumoto – PLoS One

Review: Advances in Gut Microbiome Research, Opening New Strategies to Cope with a Western Lifestyle – Gina P. Rodriguez-Castaño – Frontiers in Genetics

Animal experiments 

Effect of Lactobacillus Strains on Intestinal Microflora and Mucosa Immunity in Escherichia coli O157:H7-Induced Diarrhea in Mice – Xin Bian  – Current Microbiology

Modulation of gut microbiota and increase in fecal water content in mice induced by administration of Lactobacillus kefiranofaciens DN1 -Dana Jeong – Food & Function

Plant, root, and soil microbiome

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland – Theresa A. McHugh- Environmental Microbiology

Water and extremophile microbiome

Temporal and Spatial Variations of Bacterial and Faunal Communities Associated with Deep-Sea Wood Falls – Petra Pop Ristova – PLoS One

Probiotics / prebiotics

*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

Changes in the Gut Microbiota After Early Administration of Oral Synbiotics to Young Infants in India – DS Chandel -Journal of Pediatric Gastroenterology Nutrition

Techniques

Home-made cost effective preservation buffer is a better alternative to commercial preservation methods for microbiome research – Sebastian Menke- Frontiers in microbiology

Furosemide enhances the sensitivity of urinary metabolomics for assessment of kidney function – Isaie Sibomana – Metabolomics

Impact of sample processing on human airways microbial metagenomes – Lutz Wiehlmann – Journal of Biotechnology

Microbes in the news 

Scientists develop new flu vaccines for dogs

New Insight Describes Connection between Salmonella Infection and Appetite Loss

Anitha’s non-microbiology picks

Tiny Satellites to Make Big Contributions to Science

First report of metallic hydrogen on earth – Hydrogen turned into metal in stunning act of alchemy that could revolutionise technology and spaceflight

January 26, 2017

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Environmental ecology review presents how microbial life strategy concepts are applied in complex microbial communities.   Two interesting model systems are described in the techniques section, plus potentially scalable workflow for the preparation of high potency Akkermansia muciniphila cells for therapeutic interventions.  The importance of understanding the role of the microbiome in preventing complications after organ transplant and surgeries are discussed in two reviews.   Another study shows that proton pump inhibitors used to prevent gastric ulcers were associated with distinct gut microbiota signatures.  For faster wound healing, try some saliva. A study shows the beneficial effects of saliva on wound healing in human epidermal keratinocytes and on the attenuation of intracellular Staph. aureus infection.

Pregnancy and early life

Assessment of the synbiotic properties of human milk oligosaccharides and Bifidobacterium longum subsp. infantis in vitro and in humanised mice – S Musilova- Beneficial Microbes

Multi-site human microbiome

Review: Infection in Organ Transplantation – Jay A. Fishman – American Journal of Transplantation

Review: The gut microbiome and the mechanism of surgical infection – J.C. Alverdy – The British Journal of Surgery

Human Oral Microbiome

Salivary mucins promote the coexistence of competing oral bacterial species – Erica Shapiro Frenke- The ISME Journal

Human skin microbiome

Saliva induces expression of antimicrobial peptides and promotes intracellular killing of bacteria in keratinocytes by epidermal growth factor receptor transactivation – T. Mohanty – British Journal of Dermatology

Human gut microbiome

The influence of proton pump inhibitors and other commonly used medication on the gut microbiota – Floris Imhann – Gut Microbes

Animal experiments

Review: Understanding host-microbial interactions in rumen: searching the best opportunity for microbiota manipulation – Nilusha Malmuthuge  – Journal of Animal Science and Technology

Plant, root, and soil microbiome

Review: Revisiting life strategy concepts in environmental microbial ecology – Adrian Ho- FEMS Microbiology Ecology

Diclofop-methyl affects microbial rhizosphere community and induces systemic acquired resistance in rice – Si Chen – Journal of Environmental Sciences

Food microbiology

Review: Human pathogens in plant biofilms: Formation, physiology, and detection – Eduardo Ximenes – Biotechnology and Bioengineering

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork -Koji Yahara – Environmental Microbiology

Digestive fate of dietary carrageenan: Evidence of interference with digestive proteolysis and disruption of gut epithelial function – Lulu Fahoum – Molecular Nutrition Food Research

Bioinformatics

It’s a big data problem: researchers from the University of California, San Diego and the J.C. Venter Institute used machine learning to teach a computer to learn to distinguish between healthy and unhealthy gut microbiomes. The new approach shows promise for predicting related health issues and providing guidance for therapy development. More from the press

Techniques

Preparation and preservation of viable Akkermansia muciniphila cells for therapeutic interventions – JP Ouwerkerk  -Beneficial Microbes

Evaluation of colonization resistance in stool of human donors using ex vivo, in vitro and in vivo assays – MF Galvão  – Beneficial Microbes

Improving metabolite production in microbial co-cultures using a spatially constrained hydrogel – Matthew J. Smith – Biotechnology and Bioengineering

Microbes in the news

CRISPR research institute expands into agriculture, microbiology

Dog obesity, a growing problem, may be managed through diet and exercise and- microbiology

Every surfer knows you should stay out of the water for 72 hours after it rains. Public health officials issued an advisory for all Los Angeles County beaches, cautioning swimmers and surfers to stay away from areas near storm drains, creeks and rivers. But when the waves show – some surfers just can’t help themselves.

January 25, 2017

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Joint opinion on measures by the EU to reduce antimicrobial agents in animal husbandry, diet changes the gut microbiome of dogs, and synthetic chemicals might drive global climate change.

Jobs

PhD Position: THE ROLE OF THE GUT MICROBIOME IN LIVER DISEASE: DEVELOPMENT Of BIOINFORMATIC APPROACHES TO IDENTIFY, CHARACTERISE AND ANALYSE THE GUT VIROME – KU Leuven

Postdoctoral Research Scientist, Microbiology, School of Natural Sciences, NUI Galway

Microbiology Supervisor – Clinical Pathology Laboratories, Inc

General microbiology and policy

Artificial bacteria: A semisynthetic organism engineered for the stable expansion of the genetic alphabet – Yorke Zhang – PNAS

Policy opinions: EMA and EFSA Joint Scientific Opinion on measures to reduce the need to use antimicrobial agents in animal husbandry in the European Union, and the resulting impacts on food safety (RONAFA) – CVMP and BIOHAZ – EFSA Journal

Acid-suppression medications and bacterial gastroenteritis: a population-based cohort study – Wei Li – british journal of clinical pharmacology

Animal experiments

Effects of the Dietary Protein and Carbohydrate Ratio on Gut Microbiomes in Dogs of Different Body Conditions – Qinghong Li – mBio

Water and extremophile microbiome

Novel Primer Sets for Next Generation Sequencing-Based Analyses of Water Quality – Elvina Lee – PLoS One

Evaluation of Methods for the Concentration and Extraction of Viruses from Sewage in the Context of Metagenomic Sequencing – Mathis Hjort Hjelmsø – PLoS One

Phages and viruses

FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems – Luis Jose Rene Arredondo-Hernandez – PLoS One

The Complete Genome Sequence of a Second Distinct Betabaculovirus from the True Armyworm, Mythimna unipuncta – Robert L. Harrison – PLoS One

Characterization and Genetic Variation of Vibrio cholerae Isolated from Clinical and Environmental Sources in Thailand – Achiraya Siriphap – PLoS One

Bioinformatics

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective – Not Only Size Matters! – John Vollmers – PLoS One

Microbes in the news

Study: Babies’ Microbiomes Indifferent to Mode of Delivery – Kerry Grens – The Scientist

About FishTaco: Microbiome as complex as previously thought – Julian Harris – PHG Foundation

Auckland’s water shock: Bacteria levels ‘dangerously high’ – NZ Herald

For healthier buildings, just add bacteria? – Ed Yong – Ted

Xin’s non-microbiology pick

Synthetic chemicals as agents of global change – Emily S Bernhardt – Frontiers in Ecology and the Environment

January 22, 2017

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Events and Jobs

PhD scholarship in Molecular Microbiology– University of Copenhagen-Last Date: February 8, 2017

Quality Control Associate-Microbiology–US-CA-Del Mar

General Microbiome

Impacts of chemical gradients on microbial community structure-Jianwei Chen-The ISME Journal

Human Skin

Proteomic and peptidomic analysis of human sweat with emphasis on proteolysis-Yijing Yu-Journal of Proteomics

Human Respiratory Microbiome

Nasopharyngeal Microbiome Diversity Changes over Time in Children with Asthma–Marcos Pérez-Losada-PLOS One

Adherence of Pseudomonas aeruginosa to cystic fibrosis buccal epithelial cells–Meike Lingner-ERJ

Human Vaginal Microbiome

The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk-Lindsay M. Kindinger-Microbiome

Human Gut Microbiome

Role of Gastrointestinal Microbiota on Kidney Injury and the Obese Condition-Keerati Wanchai-The American Journal of the Medical Sciences

Review-Altered Molecular Signature of Intestinal Microbiota in Irritable Bowel Syndrome Patients Compared with Healthy Controls: a Systematic Review and Meta-analysis-Hai Ning Liu-Digestive and Liver Disease

Animal Microbiome

Bacterial community composition and fermentation in the rumen of Xinjiang brown cattle (Bos taurus), Tarim red deer (Cervus elaphus yarkandensis), and Karakul sheep (Ovis aries)-Wenxi Qian-Canadian Journal of Microbiology

The Gut Microbiome of the Vector Lutzomyia longipalpis Is Essential for Survival of Leishmania infantum–Stephen M. Beverley-mBio

The normal vaginal and uterine bacterial microbiome in giant pandas (Ailuropoda melanoleuca)-Xin Yang-Microbiological Research

Pathogen-mediated manipulation of arthropod microbiota to promote infection–Nabil M. Abraham-PNAS

The gastrointestinal tract of farmed mink (Neovison vison) maintains a diverse mucosa-associated microbiota following a 3-day fasting period-Martin I. Bahl-Microbiology Open

Ovarian cycling and reproductive state shape the vaginal microbiota in wild baboons–Elizabeth A. Miller-BMC Microbiome

Plant, root, and soil microbiome

A decade of irrigation transforms the soil microbiome of a semi-arid pine forest-Martin Hartmann-Molecular Ecology

Methane Emissions and Microbial Communities as Influenced by Dual Cropping of Azolla along with Early Rice-Jingna Liu-Scientific Reports

Differential responses of soil bacterial communities to long-term N and P inputs in a semi-arid steppe-Ning Ling-Geoderma

Mineralization of “non-metabolizable” glucose analogues in soil: potential chemosensory mimics of glucose-Kyle Mason-Jones-Journal of Plant Nutrition and Soil Science

Deciphering composition and function of the root microbiome of a legume plant-Kyle Hartman-BMC Microbiome

Isolation and characterization of Rhizobium sp. strain YS-1r that degrades lignin in plant biomass-Colin A. Jackson-Journal of Applied Microbiology

Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil–Lateef B. Salam-Environmental Science and Pollution Research

Biocontrol effects of Brevibacillus laterosporus AMCC100017 on potato common scab and its impact on rhizosphere bacterial communities-Shengfu Chen-Biological Control

Co-inoculation with Enterobacter and Rhizobacteria on Yield and Nutrient Uptake by Wheat (Triticum aestivum L.) in the Alluvial Soil Under Indo-Gangetic Plain of India-Ashok Kumar-Journal of Plant Growth Regulation

 Ornamental flowers in new light: Artificial lighting shapes the microbial phyllosphere community structure of greenhouse grown sunflowers (Helianthus annuus L.)–Beatrix W. Alsanius–Scientia Horticulturae

Extremophiles

Phylogenomics of Rhodobacteraceae reveals evolutionary adaptation to marine and non-marine habitats-Meinhard Simon-ISME

Review: Marine Bacterioplankton Seasonal Succession Dynamics-Carina Bunse-Trends in Microbiology

Review: Stress response physiology of thermophiles–Preeti Ranawat-Archives of Microbiology

The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights-Emanuele Bosi-BMC Genomics

Sulfur compound oxidation and carbon co-assimilation in the haloalkaliphilic sulfur oxidizers Thioalkalivibrio versutus and Thioalkalimicrobium aerophilum-Wee Kiong Ang-Research in Microbiology

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman–Kaitlin R. Rempfert-Extreme Microbiology

Microbial character related sulfur cycle under dynamic environmental factors based on the microbial population analysis in sewerage system-Qian Dong-Aquatic Microbiology

Similar community assembly mechanisms underlie similar biogeography of rare and abundant bacteria in lakes on Yungui Plateau, China-Jingqiu Liao-Limnology and Oceanography

Unraveling the microbial processes of black band disease in corals through integrated genomics-Yui Sato-Scientific Reports

Preliminary Phylogenetic Analysis of Thermophilic Bacteria Producing Protease isolated from Kuantan Malaysia -Essam A. Makky-JBSR

Identification of a novel fatty acid in the cell membrane of Chryseobacterium frigidisoli PB4T isolated from an East Antarctic glacier forefield-Kai Mangelsdorf-Organic Geochemistry

Phosphorus removal by marine bacterium enhanced with iron in the presence of silicon–Yanru Wang-Journal of Chemical Technology and Biotechnology

 Built Environment Microbiology

Developing Evidence-based Tools for Designing and Evaluating Hospital Inpatient Rooms–Xiaobo Quan-Journal of Interior Design

Building-related symptoms are linked to the in vitro toxicity of indoor dust and airborne microbial propagules in schools: A cross-sectional study-J T Salin-Environmental Research

Techniques

Review:  Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism-Robert J. Wallace-Genetics Selection Evolution

Balance Trees Reveal Microbial Niche Differentiation–James T. Morton-Ecological and Evolutionary Science

Virus

Review: Virus–host interactions and their roles in coral reef health and disease–Rebecca Vega Thurber-Nature Reviews Microbiology

Virome of US bovine calf serum-Mohammadreza Sadeghi-Biologicals

More Microbes

Bacillus zeae sp. nov. isolated from the rhizosphere of Zea mays– Peter Kämpfer-International Journal of Systematic and Evolutionary Microbiology

Microbes in News

Capnophilic Enterobacteriaceae-JM. Sahuquillo Arce-Diagnostic Microbiology and Infectious Disease

January 18, 2017

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Biogeographical patterns and assembly processes of bacterial on glaciers. And, a critical review of interactions between central nervous system and microbiota during health and neurological disease.

● Hospital microbiome

Microbiota-targeted therapies on the intensive care unit. Haak, BW . Current opinions in Critical Care

● Human microbiome and nervous system

Review: Interactions between the microbiota, immune and nervous systems in health and disease. Thomas C Fung.Nature Neuroscience

● Human gut microbiome

A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Patrascu O. Scientific Report

Fecal microbiota transplantation to fight Clostridium difficile infections and other intestinal diseases. Moelling, K. Bacteriophage

● Animal experiments 

Pepsin egg white hydrolysate modulates gut microbiota in Zucker obese rats. Requena T. Food & Function

Effect of early antibiotic administration on cecal bacterial communities and their metabolic profiles in pigs fed diets with different protein levels. Zhang C. Anaerobe

● Animal microbiome 

Fiber degradation potential of natural co-cultures of Neocallimastix frontalis and Methanobrevibacter ruminantium isolated from yaks (Bos grunniens) grazing on the Qinghai Tibetan Plateau. Wei YQ. Anaerobe

Gut microbiota isolated from the European pond turtle (Emys orbicularis) and its antimicrobial resistance. Ruzauskas M. Polish Journal of Veterinary Sciences

● Plant, root, and soil microbiome

Restoration using Azolla imbricata increases nitrogen functional bacterial groups and genes in soil. Xiao-Ming Lu. Applied Microbiology and Biotechnology

Ectomycorrhizal fungal diversity associated with endemic Tristaniopsis spp. (Myrtaceae) in ultramafic and volcano-sedimentary soils in New Caledonia. Waseem M. Mycorrhiza

Diversity and Assembling Processes of Bacterial Communities in Cryoconite Holes of a Karakoram Glacier.Ambrosini, R.Microbial Ecology

● Water and extremophile microbiome 

Bacterial community structure and prevalence of Pusillimonas-like bacteria in aged landfill leachate. Remmas, N. Environmental Science and Pollution Research