Category Archives: Human respiratory

December 13, 2017

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Many interesting articles today: Probiotics can inhibit human colonic smooth muscle contraction in vitro in a dose dependent manner, arsenic exposure early in life alters the gut microbiome and can increase E.coli resistance genes, oral administration of two probiotics in mice has specific effects on gene expression in the small intestine, a detailed investigation of the impacts of T. congolense infection in the tsetse fly, and multiple articles on plant and rhizosphere microbiome volatiles.

Events and jobs

Visiting Professor (Part Time) Microbiology  – Chamberlain College of Nursing, Jacksonville, FL Campus

Seminar: The “Bedside to Bench and Back Again” Paradigm in Gut Microbiome Research – Gary D. Wu – University of Chicago

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General microbiome

Review: Hygiene Hypothesis in Asthma Development: Is Hygiene to Blame? – Erik van Tilburg Bernardes – Archives of Medical Research

Human respiratory microbiome

Composition and variation of respiratory microbiota in healthy military personnel – Jun Hang – PLOS One

Human oral microbiome

Periodontitis is associated with significant hepatic fibrosis in patients with non-alcoholic fatty liver disease – William Alazawi – PLOS One

Human gut microbiome

Hypoxia and inactivity related physiological changes precede or take place in absence of significant rearrangements in bacterial community structure: The PlanHab randomized trial pilot study – Robert Šket – PLOS One

*Arsenic exposure and intestinal microbiota in children from Sirajdikhan, Bangladesh – Xiaoxi Dong – PLOS One

Editorial overview: Gastrointestinal: New frontiers in therapeutics for GI diseases and disorders — from microRNAs to novel pharmaceutics, to low FODMAP diets and microbiome – Fievos L Christofi – Current Opinion in Pharmacology

*Inhibition effect of Bifidobacterium longum, Lactobacillus acidophilus, Streptococcus thermophilus and Enterococcus faecalis and their related products on human colonic smooth muscle in vitro – Jing Gong – PLOS One

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Animal experiments

*The distinct effects of orally administered Lactobacillus rhamnosus GG and Lactococcus lactis subsp. lactis C59 on gene expression in the murine small intestine – Chise Suzuki – PLOS One

Diversity of intestinal bacterial lactase gene in antibiotics-induced diarrhea mice treated with Chinese herbs compound Qi Wei Bai Zhu San – Lu He – 3 Biotech

The Impact of Long-Term Intake of Phenolic Compounds-Rich Grape Pomace on Rat Gut Microbiota – Stéphanie Chacar – Journal of Food Science

Preprint: High-dimensional microbiome interactions shape host fitness – Alison L Gould – bioRxiv

Animal microbiome

Comparison of the intestinal mucosal microbiota in dogs siagnosed with idiopathic inflammatory bowel disease and dogs with food-responsive diarrhea before and after treatment – K. Kalenyak – FEMS Microbiology Ecology

*Molecular characterization of tsetse’s proboscis and its response to Trypanosoma congolense infection – Erick O. Awuoche – PLOS Neglected Tropical Diseases

Preprint: Who is the host of the host-associated microbiome? Colony-level dynamics overshadow individual-level characteristics in the fur microbiome of a social mammal, the Egyptian fruit-bat – oren kolodny – BioRxiv

Plant, root, and soil microbiome

Pontibacter brevis sp. nov., isolated from rhizosphere soil of Tamarix ramosissima – Ghenijan Osman – International Journal of Systemic and Evolutionary Microbiology

*Volatiles in the Rhizosphere: Bioprospecting for Sustainable Agriculture and Food Security – Shyamalina Haldar – In: Volatiles and Food Security. Springer

*Characterization of Bacterial Volatiles and Their Impact on Plant Health Under Abiotic Stress – Anukool Vaishnav – In: Volatiles and Food Security. Springer

Dissertation: Plant growth-promoting rhizobacteria (PGPR) mediate interactions between abiotic and biotic stresses in cool- and warm-season grasses – Richard Coy – Auburn University

Endophytic Microorganisms: Promising Candidate as Biofertilizer – Manish Kumar – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 6. Springer

*Bacterial Volatiles in Promotion of Plant Under Biotic Stress – Shekhar Jain – In: Volatiles and Food Security. Springer

*Microbial Volatiles in Defense – Monika – In: Volatiles and Food Security. Springer

*Microbial Volatiles and Plant Defense – Kalaivani K. Nadarajah – In: Volatiles and Food Security. Springer

Wonders of Microbes in Agriculture for Productivity and Sustainability – Rajababu V. Vyas – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 6. Springer

Water and extremophile microbiome

Review: Marine microbiology: Illuminating the importance of nitrite oxidation – Ursual Hofer – Nature Reviews Microbiology

Microbial Ecology

Robustness of a model microbial community emerges from population structure among single cells of a clonal population – Anne W. Thompson – Environmental Microbiology

Resource availability modulates biodiversity-invasion relationships by altering competitive interactions – Tianjie Yang – Environmental Microbiology

Resistome

Action mechanism of naphthofuranquinones against fluconazole-resistant Candida tropicalis strains evidenced by proteomic analysis: The role of increased endogenous ROS – João Batista de Andrade Neto – Microbial Pathogenesis

Evolution of virulence in Enterococcus faecium, a hospital-adapted opportunistic pathogen – Wei Gao – Current Opinion in Microbiology

Surveillance of antibiotic resistance among common Clostridium difficile ribotypes in Hong Kong – Viola C. Y. Chow – Scientific Reports

Food microbiology

Preprint: Copy number variation in fungi and its implications for wine yeast genetic diversity and adaptation – Jacob Steenwyk – bioRxiv

More Microbes

Draft genome sequence of Actinotignum schaalii DSM 15541T: Genetic insights into the lifestyle, cell fitness and virulence – Atteyet F. Yassin – PLOS one

PsrA controls the synthesis of the Pseudomonas aeruginosa quinolone signal via repression of the FadE homolog, PA0506 – Greg Wells – PLOS one

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Phages and viruses

Dissertation: Uncovering the Biological Features of Unknown Viruses Using Shotgun Metagenomic Sequence Data – Daniel Joseph Nasko – University of Delaware

Bioinformatics

MPA Portable: a Stand-alone Software Package for Analyzing Metaproteome Samples on the Go – Thilo Muth – Analytical Chemistry

Dissertation: Revealing Microbial Responses to Environmental Dynamics: Developing Methods for Analysis and Visualization of Complex Sequence Datasets – Matthew Kellom – Arizona State University

Preprint: Rarefaction, alpha diversity, and statistics – Amy Willis – bioRxiv

Biotechnology

Review: Electron transport phenomena of electroactive bacteria in microbial fuel cells: a review of Proteus hauseri – I-Son Ng – Bioresources and Bioprocessing

Dissertation: From Biofuels to Natural Products: Microbial Metabolic Engineering for Chemical Production – Nicole E Nozzi -University of California, Davis

Waste and Pollution

Assessment of a novel anti-biofouling microorganism (Bacillus sp. T5) for control of membrane biofouling and its effect on bacterial community structure in membrane bioreactors – Bahar Yavuztürk Gül – Water Science and Technology

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Microbes in the news

New Data: 2 Million Puerto Ricans Risk Water Contamination – Mekela Panditharatne – NRDC

Bacteria development marks new era in cellular design – Phys.org

Feeding Overcrowded Bacteria Increases Antibiotic Susceptibility – Genetic Engineering and Biotechnology News

A Bacterial Role In High Blood Pressure – The Microbiome Speaks – Chuck Dinerstein – American Council on Science and Health

New Microbiome Analysis Tool Resolves Individual Species, Strains – Rachel Lutz – MD Magazine

How honey bee gut bacteria help to digest their pollen-rich diet – EurekaAlert

Microbes on the market

Bio-Rad Inks Supply and Distribution Agreement for Microbiome MDx – genomeweb

Dannon, as a part of DanoneWave Public Benefit Corporation, Announces $50K in Grants for Graduate Studies – Markets Insider

 

December 11, 2017

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Today’s digest is quiet a treat- A microbiome survey of emergency medical service personnel (EMS), a Python release of Mothur, and a global recall of baby formula over contamination scares ( Lactalis )

General Microbiome

 The Emergency Medical Service Microbiome. Hudson AJ. Applied Environmental Microbiology

 Human Gut Microbiome

Towards utilization of the human genome and microbiome for personalized nutrition. Bashiardes S. Current Opinions in Biotechnology

Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China. Ren Z. Oncotarget.

Lung Microbiome

The distal airway microbiome after lung transplantation: A driver of immune regulation? Mitchell AB. Journal of Heart and Lung Transplant

Plant, water, and soil microbiome

 Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber. Salomez M. Journal of Applied Microbiology

Microbial ecology of the Agaricus bisporus mushroom cropping process.McGee CF. Applied Microbiology and Biotechnology

A new niche for anoxygenic phototrophs as endoliths. Roush D. Applied Environmental Microbiology

Animal experiments and microbiome

Co-occurrence of early gut colonization in neonatal piglets with microbiota in the maternal and surrounding delivery environments.Chen X. Anaerobe.

Techniques/Protocol

Metabolic Model Reconstruction and Analysis of an Artificial Microbial Ecosystem. Ye C. Methods in Molecular Biology

mothur-py 0.3.0

-PyPI

Microbes in the NEWS

‘Extremophile’ Antarctic Bacteria Could Unlock Secret to Alien Life (VIDEO)

-Sputnik International

French baby-milk maker Lactalis orders major product recall over bacteria fears

-Prothom Alo (English)

 

 

 

December 5, 2017

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Today we have interesting reviews, one about proteomics and human microbiome by C.A. Kolmedar, the other about oral microbiome by L.P.Shaw and the third about human gut virome by L.A. Ogilvie. In Water section you can read the study by V.J. Koles who developed a model that simulates metagenomes and metatranscriptomes for comparison with observations. In section Bioinformatics you can read about new tools MetaLab and ASAR while in non-microbiology pics you can check podcast “Dances with rocks” with A. Denton, geologist and planetary scientist who wants to dance on Mars. Enjoy!

Jobs

Microbiology Supervisor, Rockville, Maryland

Associate Bioengineer II, Analytical R&D, Warren, NJ

Events

9th Congress of Microbiology and Parasitology Kicks Off in Cuba

General microbiome

Microbially Mediated Electrosynthesis Processes – Mohita Sharma – Microbial Fuell Cell

Development of Suitable Anode Materials for Microbial Fuel Cells – Thi Hiep Han – Microbial Fuel Cell

Progress and Future Direction of Chromosome-Centric Human Proteome Project – Young-Ki Paik – Journal of Proteome Research

Review: Proteomics and the human microbiome: where we are today and where we would like to be – Carolin Adriane Kolmeder – Emerging Topics in Life Sciences

March of the Microbes: Harnessing the Power of the Human Microbiome to Improve Health and Target Disease – Helen Albert – Clinical OMICs

In vitro models of the human microbiota and microbiome – Julie A.K. McDonald – Emerging Topics in Life Sciences

Pregnancy and early life

Development of the Microbiota in Infants and its Role in Maturation of the Gut Mucosa and the Immune System – Cecilia Ximenez – Archives of Medical Research

Human nearly-sterile sites

The Influence of Age and Sex on Ocular Surface Microbiota in Healthy Adults -Xiaofeng Wen – Immunology and Microbiology

Human respiratory microbiome

Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae – David W Cleary – bioRxiv

The nasopharyngeal microbiome – David W. Cleary- Emerging Topics in Life Sciences

The lung microbiome in health and disease – Miriam F Moffatt – Clinical Medicine

New Strategies and Challenges in Lung Proteomics and Metabolomics. An Official American Thoracic Society Workshop Report – Russell P. Bowler – Annals of the American Thoracic Society

Fungal microbiota in chronic airway inflammatory disease and emerging relationships with the host immune response – Irene Zhang – Frontiers in Microbiology

Oral microbiome

Nonleachable Imidazolium-Incorporated Composite for Disruption of Bacterial Clustering, Exopolysaccharide-Matrix Assembly, and Enhanced Biofilm Removal – Geelsu Hwang – ACS Applied Materials & Interfaces

Review: The oral microbiome – Liam P. Shaw – Emerging Topics in Life Sciences

Use of Probiotics and Oral Health – Robert P. Allaker – Current Oral Health Reports

Subgingival Microbiome Colonization and Cytokine Production during Early Dental Implant Healing – Jeffrey B. Payne – mSphere

Human vaginal microbiome

The human female urogenital microbiome: complexity in normality – David A. MacIntyre – Emerging Topics in Life Sciences

Human gut microbiome

Gut microbiome production of short-chain fatty acids and obesity in children – Selvasankar Murugesan – European Journal of Clinical Microbiology & Infectious Diseases

The gut microbiome and hypertension – Pevsner-Fischer – Current Opinion in Nephrology and Hypertension

In vitro models of the human microbiota and microbiome – Julie A.K. McDonald – Emerging Topics in Life Sciences

Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota – Ibrahim Hamad – Scientific Reports

Lymphatic system and gut microbiota affect immunopathology of neuroinflammatory diseases, including multiple sclerosis, neuromyelitis optica and Alzheimer’s disease – Ikuo Tsunoda – Clinical & Experimental Neuroimmunology

Effect of different treatments and alcohol addiction on gut microbiota in minimal hepatic encephalopathy patients – Zan Zuo – Experimental and Therapeutic Medicine

Microbes Tickling Your Tummy: the Importance of the Gut-Brain Axis in Parkinson’s Disease – Paula Perez-Pardo – Current Behavioral Neuroscience Reports

Gancao-Gansui combination impacts gut microbiota diversity and related metabolic functions – Jingao Yu – Journal of Ethnopharmacology

Gut microbiome production of short-chain fatty acids and obesity in children – Selvasankar Murugesan – European Journal of Clinical Microbiology & Infectious Diseases

Gut microbiota in human SLE and a mouse model of lupus – Xin M. Luo – Applied and Environmental Microbiology

The interaction between smoking, alcohol and the gut microbiome – Gabriele Capurso – Best Practice & Research Clinical Gastroenterology

Animal experiments

Lactation-related metabolic mechanism investigated based on mammary gland metabolomics and 4 biofluids’ metabolomics relationships in dairy cows – Hui-Zeng Sun – BMC Genomics

Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform – Junhyung Kim – Gut Pathogens

Chronic glucocorticoid treatment induced circadian clock disorder leads to lipid metabolism and gut microbiota alterations in rats – Tao Wu – Life Sciences

Animal microbiome

Gut microbiota composition is associated with environmental landscape in honey bees – Julia C Jones –  Ecology and Evolution

Microbiota and environmental stress: how pollution affects microbial communities in Manila clams – M. Milan – Aquatic Toxicology

Analysis of the bacterial microbiome in the small octopus, Octopus variabilis, from South Korea to detect the potential risk of foodborne illness and to improve product management – Jin-JaeLee  – Food Research International

Plant, root, and soil microbiome

Studies on mycorrhizal biodiversity in medicinal plant species of Pookode lake area, Wayanad, Kerala, India – Saranya Babu Jayaprakash C.M. – Annals of Plant Sciences

Effects of Iron Amendments on the Speciation of Arsenic in the Rice Rhizosphere after Drainage – Noriko Yamaguchi – Soils

Continuous application of different organic additives can suppress tomato disease by inducing the healthy rhizospheric microbiota through alterations to the bulk soil microflora – Hongjun Liu – Plant and Soil

Seasonal changes in a maize-based polyculture of central Mexico reshape the co-occurrence networks of soil bacterial communities – Eria A. Rebollar – Frontiers in Microbiology

Evolution of microbial communities during electrokinetic treatment of antibiotic-polluted soil – Hongna Li – Ecotoxicology and Environmental Safety

Roles of different active metal-reducing bacteria in arsenic release from arsenic-contaminated paddy soil amended with biochar – Jiang-taoQiao – Journal of Hazardous Materials

Legume crop rotation suppressed nitrifying microbial community in a sugarcane cropping soil – Chanyarat Paungfoo-Lonhienne – Scientific Reports

Responses of soil nutrients and microbial communities to three restoration strategies in a karst area, southwest China – Dejun Li – Journal of Environmental Management

Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils – Robert Wagner – Environmental Microbiology

Water and extremophile microbiome

Ocean biogeochemistry modeled with emergent trait-based genomics – V. J. Coles – Science

Bacterial Community Profiling of Waters from Aquaculture and Non-aquaculture Sites within Taal Lake Ecosystem through 16S rDNA Analysis – Leslie Michelle M. Dalmacio – The Philippine Journal of Health Research and Development

Prokaryotic Community Composition in Arctic Kongsfjorden and Sub-Arctic Northern Bering Sea Sediments as Revealed by 454 Pyrosequencing – Yin-Xin Zeng –  Frontiers in Microbiology

Microbial communities shaped by treatment processes in a drinking water treatment plant and their contribution and threat to drinking water safety – Qi Li – Frontiers in Microbiology

Diversity of microbial communities and quantitative chemodiversity in layers of marine sediment cores from an causeway (Kaichu-Doro) in Okinawa Island, Japan – Taha Soliman – Frontiers in Microbiology

Bacterial Diversity and Biogeochemistry of Two Marine Shallow-Water Hydrothermal Systems off Dominica (Lesser Antilles) – Petra Pop Ristova – Frontiers in Microbiology

Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids – Caroline S. Fortunato –  Environmental Microbiology

Functional diversity and redundancy across fish gut, sediment and water bacterial communities – Arthur Escalas – Environmental Microbiology

Built environment

Archaeal and Bacterial Community Structure in an Anaerobic Digestion Reactor (Lagoon Type) Used for Biogas Production at a Pig Farm – Pampillón-González L – Journal of Molecular Microbiology and Biotechnology

Bacterial perspectives on the dissemination of antibiotic resistance genes in domestic wastewater bio-treatment systems: beneficiary to victim – Dong Wu – Applied Microbiology and Biotechnology

Effect of ammonia on the active microbiome and metagenome and from stable full-scale digesters – J.Ruiz-Sánchez – Bioresource Technology

Droplet distribution and airborne bacteria in an experimental shower unit – C.E.Estrada-Perez – Water Research

Food Microbiology

Environmental Microbiota Drives Microbial Succession and Metabolic Profiles during Chinese Liquor Fermentation – Xueshan Wang – Applied and Environmental Microbiology

Shotgun metagenomics and volatilome profile of the microbiota of fermented sausages -Ilario Ferrocino –  Applied and Environmental Microbiology

Probiotics / prebiotics

Bifidobacterium longum 1714 as a translational psychobiotic: modulation of stress, electrophysiology and neurocognition in healthy volunteers – A P Allen  – Translational Psychiatry

Phage and viruses

High HPV16 E6 viral load in the oral cavity is associated with an increased number of bacteria: A preliminary study – Hideo Shigeishi – Biomedical Reports

Kullback Leibler divergence in complete bacterial and phage genomes – Sajia Akhter – PeerJ

Review: The human gut virome: form and function – Lesley A. Ogilvie – Emerging Topics in Life Sciences

Deep sequencing reveals high bacterial diversity and phylogenetic novelty in pit mud from Luzhou Laojiao cellars for Chinese strong-flavor Baijiu – Mao-KeLiu – Food Research International

Bioinformatics

Accurate Determination of Bacterial Abundances in Human Metagenomes Using Full-length 16S Sequencing Reads – Fanny Perraudeau – bioRxiv

MetaLab: an automated pipeline for metaproteomic data analysis – Kai Cheng – Microbiome

ASAR: visual analysis of metagenomes in R – Askarbek Orakov – Bioinformatics

Bacteria & Biofuels

Metabolome analysis reveals a role for glyceraldehyde 3-phosphate dehydrogenase in the inhibition of C. thermocellum by ethanol – Liang Tian – Biotechnology for Biofuels

Biophotovoltaics: Conversion of Light Energy to Bioelectricity Through Photosynthetic Microbial Fuel Cell Technology – Rashmi Chandra – Microbial Fuel Cell

Techniques

Electron microscopy reveals unique nano forms of bacterial spores – Sumanta Ghosh – bioRxiv

Continuous and High-throughput Electromechanical Lysis of Bacterial Pathogens using Ion Concentration Polarization – Minseok Kim – Analytical Chemistry

Microbes in the news

A New Antibiotic Weakness—Drugs Themselves Help Bacteria Survive

Exercise Changes Gut Microbial Composition Independent of Diet, Study Shows

Bacteria and obesity: Reviewing the connection between gut bacteria, obesity, and diet

Bacteria & Art

Bacteria Collection of Icons Vector Illustration

Tina’s non microbiology picks

PODCAST: This Scientist Wants To Dance On Mars (And She Just Might Make That Happen)

How to Review a Manuscript

December 2, 2017

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Events and jobs
PhD Student – Developing and validating a computational model of the gut microbiota–mucosa interactions to replace and reduce animal experiments – Birmingham, UK

Assistant/Associate Professor, Microbiology and Immunology – SUNY Upstate Medical University – Syracuse, NY

Microbiology Manager – Cranleigh Scientific – Kent, England

Adjunct Anatomy and Physiology and Microbiology Instructor – City College – Altamonte Springs, FL

Program Manager – Rutgers, The State University of New Jersey

Assistant Professor, Statistics and Microbiology – The University of Manitoba – Winnipeg, Manitoba, Canada

Human respiratory microbiome
Making It Last: Storage Time and Temperature Have Differential Impacts on Metabolite Profiles of Airway Samples from Cystic Fibrosis Patients – Stephen Wandro – MSystems

Human skin microbiome
Effects of cosmetics on the skin microbiome of facial cheeks with different hydration levels. – Silvia Esmeralda Pérez-Topete – Microbiology Open

Propionibacterium acnes induces autophagy in keratinocytes: involvement of multiple mechanisms. – Klára Megyeri – The Journal Of Investigative Dermatology

Human oral microbiome
A comparative study of the oral microbiome compositions of healthy postmenopausal, premenopausal, and prepubertal Nigerian females, using 16s rrna metagenomics methods. – K C Anukam – Nigerian Journal Of Clinical Practice

Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers – Brandilyn A. Peters – Cancer Research

Review: Microbial colonization of the periodontal pocket and its significance for periodontal therapy. – Andrea Mombelli – Periodontology 2000

Review: Resilience of the Oral Microbiota in Health: Mechanisms That Prevent Dysbiosis. – B T Rosier – Journal Of Dental Research

Human gut microbiome
Specific substrate-driven changes in human faecal microbiota composition contrast with functional redundancy in short-chain fatty acid production. – Nicole Reichardt – The Isme Journal

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients – Andrew Brantley Hall – Genome Medicine

Characteristics of Fecal Microbiota in Pediatric Crohn’s Disease and Their Dynamic Changes During Infliximab Therapy. – Yizhong Wang – Journal Of Crohn’S & Colitis

Antibiotic Resistome in a large-scale healthy human gut microbiota deciphered by metagenomic and network analyses. – Jie Feng – Environmental Microbiology

Involvement of shared mucosal-associated microbiota in the duodenum and rectum in diarrhea-predominant irritable bowel syndrome. – Gangping Li – Journal Of Gastroenterology And Hepatology

Review: Are the decrease in circulating anti-α1,3-Gal IgG and the lower content of galactosyl transferase A1 in the microbiota of patients with multiple sclerosis a novel environmental risk factor for the disease? – Emmanuel Montassier – Molecular Immunology

Review: Combined therapies to treat complex diseases: The role of the gut microbiota in multiple sclerosis. – Laura Calvo-Barreiro – Autoimmunity Reviews

Review: Computational profiling of the gut–brain axis: microflora dysbiosis insights to neurological disorders – Nikolas Dovrolis – Briefings in Bioinformatics

Animal experiments
IL-17 is a protection effector against the adherent-invasive Escherichia coli in murine colitis. – Hai-Jia Zhang – Molecular Immunology

Changes in gut microbiota during development of compulsive checking and locomotor sensitization induced by chronic treatment with the dopamine agonist quinpirole. – Tony D Jung – Behavioural Pharmacology

Potential Impact of Metabolic and Gut Microbial Response to Pregnancy and Lactation in Lean and Diet-Induced Obese Rats on Offspring Obesity Risk. – Heather A Paul – Molecular Nutrition & Food Research

Clostridium butyricum exerts a neuroprotective effect in a mouse model of traumatic brain injury via the gut-brain axis. – H Li – Neurogastroenterology And Motility : The Official Journal Of The European Gastrointestinal Motility Society

Impacts of diarrhea on the immune system, intestinal environment, and expression of PGRPs in New Zealand rabbits – Yang Chen – PeerJ

Animal microbiome
Multi-level comparisons of cloacal, skin, feather and nest-associated microbiota suggest considerable influence of horizontal acquisition on the microbiota assembly of sympatric woodlarks and skylarks. – H Pieter J van Veelen – Microbiome

Microbiota and environmental stress: how pollution affects microbial communities in Manila clams – M. Milan – Aquatic Toxicology

Production and biotechnological potentialities of extracellular polymeric substances from sponge-associated Antarctic bacteria – Consolazione Caruso – Applied and Environmental Microbiology

Review: Wild gut microbiota protect from disease. – Francesca S Gazzaniga – Cell Research

Plant, root, and soil microbiome
Symbionts protect aphids from parasitic wasps by attenuating herbivore-induced plant volatiles. – Enric Frago – Nature Communications

Microbial decomposition is highly sensitive to leaf litter emersion in a permanent temperate stream. – Juanita Mora-Gómez – The Science Of The Total Environment

Influence of fertilizers and rice cultivation methods on the abundance and diversity of phyllosphere microbiome. – Shobit Thapa – Journal Of Basic Microbiology

Antibiotic-resistant bacteria in the guts of insects feeding on plants: prospects for discovering plant-derived antibiotics. – Katarzyna Ignasiak – Bmc Microbiology

Bacterial endosymbionts influence host sexuality and reveal reproductive genes of early divergent fungi – Stephen J. Mondo – Nature Communications

Organic amendments shift the phosphorus-correlated microbial co-occurrence pattern in the peanut rhizosphere network during long-term fertilization regimes – Yan Chen – Applied Soil Ecology

The interactive effects of arbuscular mycorrhiza and plant growth-promoting rhizobacteria synergistically enhance host plant defences against pathogens – Alejandro Pérez-de-Luque – Scientific Reports

The impact of post-fire salvage logging on microbial nitrogen cyclers in Mediterranean forest soil – Lily Pereg – Science of the Total Environment

Review: Yeast population of the Kindo Peninsula lichens – A. V. Kachalkin – Microbiology

Review: Bacterial Endophyte Colonization and Distribution within Plants – Shyam L. Kandel – Microorganisms

Review: Emerging Microbial Biocontrol Strategies for Plant Pathogens – Sharifah Farhana Syed Ab Rahman – Plant Science

Water and extremophile microbiome
Microbial life on a sand grain: from bulk sediment to single grains. – David Probandt – The Isme Journal

Tracking active groundwater microbes with D2 O labeling to understand their ecosystem function. – Martin Taubert – Environmental Microbiology

Variability of the composition of the microbial community of the deep subsurface thermal aquifer in Western Siberia – V. V. Kadnikov – Microbiology

Cyanobacterial community structure in hot water springs of Indian North-Western Himalayas: A morphological, molecular and ecological approach – Yadvinder Singh – Algal Research

Built environment
Polar solar panels: Arctic and Antarctic microbiomes display similar taxonomic profiles. – Kristie Tanner – Environmental Microbiology Reports

Microorganisms of low-temperature heavy oil reservoirs (Russia) and their possible application for enhanced oil recovery – T. N. Nazina – Microbiology

Food microbiology
Review: Cereal fiber, fruit fiber, and type 2 diabetes: Explaining the paradox. – Karen M Davison – Journal Of Diabetes And Its Complications

Probiotics / prebiotics
Exploring the Impact of Food on the Gut Ecosystem Based on the Combination of Machine Learning and Network Visualization. – Hideaki Shima – Nutrients

Translational Development of Microbiome-Based Therapeutics: Kinetics of E. coli Nissle and Engineered Strains in Humans and Nonhuman Primates. – Caroline Kurtz – Clinical And Translational Science

Phages and viruses
Distribution and Inferred Evolutionary Characteristics of a Chimeric ssDNA Virus Associated with Intertidal Marine Isopods – Kalia S. I. Bistolas – Viruses

Microbial Ecology
Recipient-Biased Competition for an Intracellularly Generated Cross-Fed Nutrient Is Required for Coexistence of Microbial Mutualists – Alexandra L. McCully – mBio

Review: Cell-cell recognition and social networking in bacteria. – Vera Troselj – Environmental Microbiology

Bioinformatics
Functional sequencing read annotation for high precision microbiome analysis. – Chengsheng Zhu – Nucleic Acids Research

Reader reaction on the fast small-sample kernel independence test for microbiome community-level association analysis. – Bin Guo – Biometrics

Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes – Bhavya Papudeshi – BMC Genomics

Resources and tools for the high-throughput, multi-omic study of intestinal microbiota – Aitor Blanco-Míguez – Briefings in Bioinformatics

Techniques
Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics – Zijuan Lai – Nature Methods

Brief guide to the analysis, interpretation and presentation of microbiota data. – Stefan Zalewski – Archives Of Disease In Childhood. Education And Practice Edition

Optimized fluorescent proteins for the rhizosphere-associated bacterium Bacillus mycoides with endophytic and biocontrol agent potential. – Yanglei Yi – Environmental Microbiology Reports

Genome Announcements
Complete Genome Sequence of Bacillus altitudinis P-10, a Potential Bioprotectant against Xanthomonas oryzae pv. oryzae, Isolated from Rice Rhizosphere in Java, Indonesia. – Anto Budiharjo – Genome Announcements

Mrakia arctica sp. nov., a new psychrophilic yeast isolated from an ice island in the Canadian High Arctic – Masaharu Tsuji – Mycoscience

Microbes in the news
New research provides insights into the skin microbiome – EurekAlert

Lab notes: The vaginal microbiome can predict whether a woman is going to have a premature baby – Scroll.in
Paper link: First-trimester vaginal microbiome diversity: A potential indicator of preterm delivery risk  (posted Nov 27, 2017)

How Bacteria Help Regulate Blood Pressure – Veronique Greenwood – Quanta Magazine

Gut Bacteria Predict Responses, Survival Time to PD-1 Cancer Immunotherapy – Bryant Furlow – Modern Medicine Network

Synthetic Glycolipids As A New Class Of Antimicrobials To Down-Regulate Cell Wall Functions – Narayanaswamy Jayaraman – Science Trends

The microbiological art of making a better sausage – Phys.Org

Will microbial protein replace meat on the table? – Digital Journal – Tim Sandle

New 3-D printed materials harness the power of bacteria – Maria Temming – Science News

Scientists Have Expanded the Genetic Code in Bacteria – Brad Jones – Futurism

Microbes on the market
Qiagen Joins French Biotech to Build the Next Generation of Microbiome Technology – Alex Dale – European Biotech News

DuPont and Ireland’s APC venture forward in microbiome-inspired pact – Will Chu – Nutra Ingredients

Rebiotix Announces Expansion of Phase 1 Trial of the Company’s Oral Capsule Microbiota Product, RBX7455, Following Successful Completion of Initial Study Arms – Markets Insider

Science, publishing, and career
Five ways to fix statistics – Jeff Leek – Nature

Tiffany’s non-microbiology picks
An Open Letter to the Senate Concerning H.R.1 and the Graduate Student Tax Provision – Alana Van Dervort
# A letter (that you can sign) against one part of the bill that passed this morning

December 1, 2017

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Happy December! Today’s digest features research articles on prion like domains in phages, effect of high salt challenge on gut microbiota and immune system. Enjoy!

Events and jobs

Assistant Professor, Statistics and Microbiology – The University of Manitoba

Program Manager, Microbiology – RWJ-Pathology-PISC

General microbiome

Review: Experimental design and quantitative analysis of microbial community multiomics – Himel Mallick – Genome Biology

Pregnancy and early life

Low Microbial Diversity and Abnormal Microbial Succession Is Associated with Necrotizing Enterocolitis in Preterm Infants – Priscila T. Dobbler – Frontiers in Microbiology

Human respiratory microbiome

Colonic Bacteroides are positively associated with trabecular bone structure and programmed by maternal vitamin D in male but not female offspring in an obesogenic environment – C R Villa – International Journal of Obesity

Human skin microbiome

Diversity of bacterial communities on the facial skin of different age-group Thai males – Alisa Wilantho – PeerJ

Human oral microbiome

Oral Health and the Oral Microbiome in Pancreatic Cancer: An Overview of Epidemiological Studies – Paige M Bracci – The Cancer Journal

Bacterial alterations in salivary microbiota and their association in oral cancer – Wei-Hsiang Lee – Scientific Reports

Human vaginal microbiome

Review : Is bacterial vaginosis a disease? – Gregor Reid – Applied Microbiology and Biotechnology

Human gut microbiome

The gut mycobiome of the Human Microbiome Project healthy cohort – Andrea K. Nash – Microbiome

Analyses of gut microbiota and plasma bile acids enable stratification of patients for antidiabetic treatment – Yanyun Gu – Nature Communications

*Salt-responsive gut commensal modulates TH17 axis and disease – Nicola Wilck – Nature

Interactions between diet and the intestinal microbiota alter intestinal permeability and colitis severity in mice – Sean R.Llewellyn – Gastroenterology

Psychobiotics: A new approach for treating mental illness? – Snigdha Misra – Critical Reviews in Food Science and Nutrition

Small Intestinal Bacterial Overgrowth: Should Screening Be Included in the Pre-fecal Microbiota Transplantation Evaluation? – Jessica R. Allegretti – Digestive Diseases and Sciences

Gut microbiota-mediated generation of saturated fatty acids elicits inflammation in the liver in murine high-fat diet-induced steatohepatitis – Shoji Yamada – BMC Gastroenterology

Animal experiments

Vertical vs. horizontal transmission of the microbiome in akey disease vector, Ixodes pacificus – Jessica Y. Kwan – Molecular Ecology

Gut Microbiome-induced Shift of Acetate to Butyrate Positively Manages Dysbiosis in High Fat Diet – Xu Si – Molecular Nutrition and Food Research

Increased cortical neuronal responses to NMDA and improved attentional set-shifting performance in rats following prebiotic (B-GOS®) ingestion – Benjamin Gronier – European Neuropsychopharmacology

Effects of Lactobacillus acidophilus on gut microbiota composition in broilers challenged with Clostridium perfringens – Zhui Li – Plos One

Doxycycline induces dysbiosis in female C57BL/6NCrl mice – Felicia D. Duke Boynton – BMC Research Notes

Animal microbiome

The effect of dietary energy and protein levels on body weight, size, and microflora of ostrich chicks – Tahereh Nikravesh-Masouleh – Tropical Animal Health and Production

Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion – Miriam E. Shiffman – PeerJ

The microbiomes of blowflies and houseflies as bacterial transmission reservoirs – Ana Carolina M. Junqueira – Scientific Reports

Plant, root, and soil microbiome

The Patterns and Drivers of Bacterial and Fungal β-Diversity in a Typical Dryland Ecosystem of Northwest China – Jianming Wang – Frontiers in Microbiology

Water and extremophile microbiome

Highlighting patterns of fungal diversity and composition shaped by ocean currents using the East China Sea as a model – Wei Li – Molecular Ecology

Microbial Reduction of Fe(III) and SO42− and Associated Microbial Communities in the Alluvial Aquifer Groundwater and Sediments – Ji-Hoon Lee – Microbial Ecology

The influence of complex fermentation broth on denitrification of saline sewage in constructed wetlands by heterotrophic nitrifying/aerobic denitrifying bacterial communities – Guiping Fu – Bioresource Technology

Amplicon-Metagenomic Analysis of Fungi from Antarctic Terrestrial Habitats – Marcelo Baeza – Frontiers in Microbiology

Microbial Community Structure and Arsenic Biogeochemistry in Two Arsenic-Impacted Aquifers in Bangladesh – Edwin T. Gnanaprakasam – mBio

Probiotics / prebiotics

Short communication: Does early-life administration of a Megasphaera elsdenii probiotic affect long-term establishment of the organism in the rumen and alter rumen metabolism in the dairy calf? – T.T.Yohe – Journal of Dairy Science

Review: Effect of Probiotic Supplementation on CD4 Cell Count in HIV-Infected Patients: A Systematic Review and Meta-analysis – Asma Kazemi – Journal of Dietary Supplements

Phages and viruses

*Prion-Like Domains in Phagobiota – George Tetz – Frontiers in Microbiology

Bacteriophage Distributions and Temporal Variability in the Ocean’s Interior – Elaine Luo – mBio

Anitha’s non-microbiology picks

Hubble in a bubble: Scallop eyes act just like tiny telescopes

Jackpot of fossilized pterosaur eggs unearthed in China

Sorry, Grumpy Cat: Study finds dogs are brainier than cats

November 26, 2017

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Events and jobs

Microbiology Technician – Companion Animal Clinic – Midwestern University – Glendale, AZ

 

General microbiome

Biogas from slaughterhouse wastewater anaerobic digestion is driven by the archaeal family Methanobacteriaceae and bacterial families Porphyromonadaceae and Tissierellaceae – CE Granada – Renewable Energy

Ferrosenescence: the iron age of neurodegeneration? – A Sfera – Mechanisms of Ageing and Development

 

Pregnancy and early life

Intestinal Microbiota Composition in Sudden Infant Death Syndrome and Age-Matched Controls – LEX Leong – The Journal of Pediatrics

 

Multi-site human microbiome

Chapter: Microbiome – M Dewar – Bladder

 

Human respiratory microbiome

Bacterial microbiota of the nasal passages across the span of human life – L Bomar – Current Opinion in Microbiology

 

 

Human gut microbiome

Review: Aging and Parkinson’s Disease: Inflammaging, neuroinflammation and biological remodeling as key factors in pathogenesis – V Calabrese – Free Radical Biology and Medicine

 

Animal experiments 

The Gut Microbiota Facilitates Drifts in the Genetic Diversity and Infectivity of Bacterial Viruses – L de Sordi – Cell Host and Microbe

Differences in the gut microbiota of dogs (Canis lupus familiaris) fed a natural diet or a commercial feed revealed by the Illumina MiSeq platform – J Kim – Gut Pathogens

Influences of quorum-quenching probiotic bacteria on the gut microbial community and immune function in weaning pigs  – J Kim – Animal Science Journal

Dietary inclusion of xylanase improves growth performance, apparent total tract nutrient digestibility, apparent ileal digestibility of nutrients and amino acids and alters gut microbiota in growing pigs – KY Lee – Animal Feed Science and Technology

Age, sex, and TNF associated differences in the gut microbiota of mice and their impact on acute TNBS colitis – AJ Kozik – Experimental and Molecular Pathology

 

Animal microbiome 

Comparative analysis of gut bacterial communities of green turtles (Chelonia mydas) pre-hospitalization and post-rehabilitation by high-throughput sequencing of bacterial 16S rRNA gene – MS Ahasan – Microbiological Research

Innate immune responses to metabolic stress can be detected in rumen fluids – E Trevisi – Research in Veterinary Science

Molecular characterization and potential sources of aqueous humor bacterial contamination during phacoemulsification with intraocular lens implantation in dogs – LCC Lacerda – Veterinary Microbiology

 

Plant, root, and soil microbiome

Anaerobic microsites have an unaccounted role in soil carbon stabilization – M Keiluweit – Nature Communications

The rhizosphere and root exudates of maize seedlings drive plasmid mobilization in soil – H Zhu – Applied Soil Ecology

Review: AMF: The future prospect for sustainable agriculture – S Basu – Physiological and Molecular Plant Pathology

Review: Modified mycotoxins: An updated review on their formation, detection, occurrence, and toxic effects – L Freire – Food and Chemical Toxicology

 

 

Food microbiology

Colonic fermentation of polyphenolics from Sea buckthorn (Hippophae rhamnoides) berries: Assessment of effects on microbial diversity by Principal Component Analysis – S Attri – Food Research International

Review: Yeast and yeast derivatives in feed additives and ingredients: Sources, characteristics, animal responses, and quantification methods – GC Shurson – Animal Feed Science and Technology

 

Probiotics / prebiotics

Turning Fruit Juice Into Probiotic Beverages – ALF Pereira – Fruit Juices

Probiotics in Newborns and Children – MW Lenfestey – Pediatric Clinics of North America

 

Phages and viruses

The gut virome of the protochordate model organism, Ciona intestinalis subtype A – BA Leigh – Virus Research

DDX3 is exploited by Arenaviruses to suppress type I interferons and favor their replication – ME  Loureiro – bioRxiv

MVP: a microbe–phage interaction database  – NL Gao – Nucleic Acids Research

Immune responses in influenza A virus and human coronavirus infections: an ongoing battle between the virus and host – J Zheng – Current Opinion in Virology

 

Bioinformatics

Deciphering the Effects of Microbiome on Plants Using Computational Methods – MS Khan – Plant Bioinformatics

Application of Bioinformatics in Understanding of Plant Stress Tolerance – J Upadhyay – Plant Bioinformatics

 

Techniques

Monitoring microbial communities using light sheet fluorescence microscopy – R Parthasarathy – Current Opinion in Microbiology

Precise and simultaneous enumeration of multiplex pathogens using multiplex polymer chain reaction coupled with a novel quantitative capillary electrophoresis – C Liu – Sensors and Actuators B: Chemical

Biomarkers of antibiotic resistance genes during seasonal changes in wastewater treatment systems  – Y-N Jiao – Environmental Pollution

 

Microbes in the news

The End is Nigh — Will Biology Doom Us or Save Us? – Labiotech.eu

Study: Common food preservative harms ‘good’ gut bacteria – The Maui News

Why you should NEVER eat off your plate after a fly lands on it: Insects’ legs and wings are teeming with bacteria from rotting carcasses and faeces – Daily Mail Online

November 25, 2017

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General microbiome

Coevolution between Mutualists and Parasites in Symbiotic Communities May Lead to the Evolution of Lower Virulence. –  PG Nelson – The American Naturalist

Survival of microbes in Earth’s stratosphere – PD Sarma – Current Opinion in Microbiology

In vitro antimicrobial activity of essential oils against enterotoxigenic Escherichia coli found in a nation-wide commercial farm survey – R Palao – Animal Production Science

 

 

Human respiratory microbiome

Bacterial microbiota of the nasal passages across the span of human life – L Bomar – Current Opinion in Microbiology

 

Human skin microbiome

Diversity of bacterial communities on the facial skin of different age-group Thai males – A Wilantho – PeerJ

 

 

Human gut microbiome

Transformation of the anticancer drug doxorubicin in the human gut microbiome – A Yan – ACS Infectious Disease

Lactobacillus acidophilus Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals – MC Theilmann – mBio

 

Animal experiments 

Alterations in gut microbiota associated with a cafeteria diet and the physiological consequences in the host. – JM Del Bas – International Journal of Obesity

 

Animal microbiome 

Prevalence survey of Toxoplasma gondii in hearts from Western Australian sows – K Hodgson – Animal Production Science

The Intestinal Microbiota of Tadpoles Differs from Those of Syntopic Aquatic Invertebrates – ML Lyra – Microbial Ecology

Characterization of the upper and lower respiratory tract microbiota in Piedmontese calves – I Nicola – Microbiome

Update: The microbiome of dogs and cats – what do we know in 2017?  – C Noli – Revue Vétérinaire Clinique

Age-related differences in the respiratory microbiota of chickens – L Glendinning – PLoS One

Species-specific signatures of the microbiome from Camponotus and Colobopsis ants across developmental stages. – MO Ramalho – PLoS One

Wolbachia infection alters the relative abundance of resident bacteria in adult Aedes aegypti mosquitoes, but not larvae. – MD Audsley – Molecular Ecology

Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome. – K Raymann – Molecular Ecology

Gut microbes limit growth in House Sparrows nestlings (Passer domesticus), but not through limitations in digestive capacity. – KD Kohl – Integrative Zoology

 

Plant, root and soil microbiome

Fungal Endophyte Communities in Begonia Species from the Brazilian Atlantic Rainforest – AML Correia – Current Microbiology

Effects of silver-graphene oxide nanocomposites on soil microbial communities – M-J Kim – Journal of Hazardous Materials

Characterization of cellulolytic microbial consortium enriched on Napier grass using metagenomic approaches – P Kanokratana – Journal of Bioscience and Bioengineering

Microbial competition for nitrogen and carbon is as intense in the subsoil as in the topsoil – DL Jones – Soil Biology and Biochemistry

Warming, shading and a moth outbreak reduce tundra carbon sink strength dramatically by changing plant cover and soil microbial activity. – MB Dahl – Scientific Reports

 

Water microbiome and extremophile 

Review: Microbial mat ecosystems: Structure types, functional diversity, and biotechnological application – CM Prieto-Barajas – Electronic Journal of Biotechnology

Gelidatrema psychrophila sp. nov., a novel yeast species isolated from an ice island in the Canadian High Arctic – M Tsuji – Mycoscience

 

Built environment 

Aspergillus subgenus Polypaecilum from the built environment – JB Tanney – Studies in Mycology

Enrichment of syngas-converting communities from a multi-orifice baffled bioreactor – AL Arantes – Microbial Biotechnology

 

Food microbiology

Influence of heat processing on the volatile organic compounds and microbial diversity of salted and vacuum-packaged silver carp (Hypophthalmichthys molitrix) fillets during storage – D Li – Food Microbiology

 

Phages and viruses

Two new viruses, MCV1 and MCV2, which infect Marinitoga bacteria isolated from deep-sea hydrothermal vents: Functional and genomic analysis – C Mercier – Environmental Microbiology

 

Techniques

A potential new species of porcine Actinobacillus defined by multi-locus sequence analysis – C Turni – Animal Production Science

Evaluation of two real time PCR assays for the detection of bacterial DNA in amniotic fluid – PG de Velasco-Sada – Journal of Microbiological Methods

Discrete False-Discovery Rate Improves Identification of Differentially Abundant Microbes – L Jiang – mSystems

Stripping flow cytometry: How many detectors do we need for bacterial identification? –  P Rubbens – Cytometry A

 

Microbes in the news

Bacterial Art Starts a Debate on Money and International Borders – Labiotech.eu

Superbugs And Rockets Side By Side At Science Museum – Londonist

November 21, 2017

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A review discussing metabolic-flux dependent regulation in microbes, diversity of coral-associated viral communities, what an Antarctic fungus can tell us about astrobiology.

General microbiome

Pre-print: Extending species-area relationships (SAR) to diversity-area relationships (DAR)© – Zhanshan Ma – aRxiv

Beneficial microbiomes: Biodiversity and potential biotechnological applications for sustainable agriculture and human health – Ajar Nath Yadav – Journal of Applied Biology and Biotechnology

Pregnancy and early life

Transmission and persistence of IncF conjugative plasmids in the gut microbiota of full-term infants – Anuradha Ravi – FEMS Microbiology Ecology

Human respiratory microbiome

Pre-print: Dynamics of the upper airway microbiome in the pathogenesis of asthma-associated persistent wheeze in preschool children – Shu Mei Teo – bioRxiv

Human gut microbiome

Pre-print: A perturbation model of the gut microbiome’s response to antibiotics – Liam P Shaw – bioRxiv

Animal experiments

Pre-print: Within host selection for faster replicating bacterial symbionts – Ewa Chrostek – bioRxiv

Plant, root, and soil microbiome

Molecular characterization of Associative N2 fixing bacterium isolated from the roots of Finger millet (Eleusine coracana L.) and its interaction effects with microbial consortia on growth and yield – G B Santosha Gowda – Research Journal of Biotechnology

Significance of temperature and water availability for soil phosphorus transformation and microbial community composition as affected by fertilizer sources – Dasheng Sun – Biology and Fertility of Soils

Water and extremophile microbiome

Prokaryotic diversity and biogeochemical characteristics of benthic microbial ecosystems at La Brava, a hypersaline lake at Salar de Atacama, Chile – Maria Eugenia Farias – PLOS ONE

Phylogenetic diversity and distribution of bacterial and archaeal amoA genes in the East China Sea during spring – Takafumi Kataoka – Archives of Microbiology

Microbes in space

Resistance of an Antarctic cryptoendolithic black fungus to radiation gives new insights of astrobiological relevance – Laura Selbmann – Fungal Biology

Phages and viruses

Pre-print: Coral-associated viral communities show high levels of diversity and host auxiliary functions – Karen D Weynberg – PeerJ

Biological Control of Pectobacterium carotovorum Via Specific Lytic Bacteriophage – Eman Marei – Journal of Basic and Applied Scientific Research

Bioinformatics

Book chapter: Chapter 1 – Metagenomics: A Paradigm Shift in Microbiology – Andrey V Mardanov – Metagenomics

More microbes

Review: Metabolic-flux dependent regulation of microbial physiology – Athanosios Litsios – Current Opinion in Microbiology

Microbes in the news

High-salt diet throws microbiome out of whack – Katharine Sanderson – Chemical & Engineering News

Rare Bacterial Taxa May Play Outsize Role in Soil Microbiome Structure, Study Suggests – Genome Web

Forsyth Institute researcher Floyd Dewhirst named as AAAS Fellow – EurekAlert

What makes soil, soil? Researchers find hidden clues in DNA – Phys.Org

Microbes on the market

PathoQuest Announces Formation of Scientific Advisory Board – Business Wire

November 19, 2017

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A large number of papers overall, but especially in the plant/soil microbiome and animal experiments. For the former, one is from one of the MicrobiomeDigest contributors (in green) – congratulations!

General microbiome
Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities – Ali R. Zomorrodi – Nature Communications

Pregnancy and early life
Low dietary fiber intake increases Collinsella abundance in the gut microbiota of overweight and obese pregnant women – Luisa F. Gomez-Arango – Gut Microbes

Multi-site human microbiome
The Akkermansia-muciniphila is a gut microbiota signature in psoriasis – LiRong Tan – Experimental Dermatology

Human respiratory microbiome
Airway microbiota across age and disease spectrum in cystic fibrosis – Edith T. Zemanick – European Respiratory Journal

Human skin microbiome
Review: Skin barrier and microbiome in acne – M. A. Rocha – Archives of Dermatological Research

Fungi in the Wound Microbiome – Lindsay Kalan – Advances in Wound Care

Environmental influences on the skin microbiome of humans and cattle in rural Madagascar – Melissa B. Manus – Evolution, Medicine, and Public Health

Human gut microbiome
The Inuit gut microbiome is dynamic over time and shaped by traditional foods –
Geneviève Dubois – Microbiome

Identifying predictive features of Clostridium difficile infection recurrence before, during, and after primary antibiotic treatment – Sepideh Pakpour – Microbiome

Gastrointestinal and Hepatic Disease in Spondyloarthritis – Liron Caplan – Rheumatic Disease Clinics of North America

Review: Gutsy Moves: The Amygdala as a Critical Node in Microbiota to Brain Signaling – Caitlin S. M. Cowan – BioEssays

Review: The Role of the Gut Microbiome in Multiple Sclerosis Risk and Progression: Towards Characterization of the “MS Microbiome” – Anne-Katrin Pröbstel – Neurotherapeutics

Review: The gut–brain interaction in opioid tolerance – Hamid I Akbarali – Current Opinion in Pharmacology

Review: Lipotoxicity and the gut-liver axis in NASH pathogenesis – Fabio Marra – Journal of Hepatology

Review: Evidence of giant viruses of amoebae in the human gut – Philippe Colson -Human Microbiome Journal

Animal experiments
Evaluating the impact of domestication and captivity on the horse gut microbiome – Jessica L. Metcalf – Scientific Reports

Changes of gut microbiota structure and morphology in weaned piglets treated with fresh fermented soybean meal – Zhengjun Xie – World Journal of Microbiology and Biotechnology

Brown rice and retrograded brown rice alleviate inflammatory response in dextran sulfate sodium (DSS)-induced colitis mice – Kemika Praengam – Food and Function

Depletion of Stercobilin in Fecal Matter from a Mouse Model of Autism Spectrum Disorders – Emily R. Sekera – Metabolomics

Comparison of (R)-ketamine and lanicemine on depression-like phenotype and abnormal composition of gut microbiota in a social defeat stress model – Youge Qu – Scientific Reports

Beyond immunity: The Imd pathway as a coordinator of host defense, organismal physiology and behavior – Zongzhao Zhai – Developmental & Comparative Immunology
# This is a review on the Imd pathway in Drosophila, and its influence on their gut microbiome.

Dietary Fructo-Oligosaccharides Attenuate Early Activation of CD4+ T Cells Which Produce both Th1 and Th2 Cytokines in the Intestinal Lymphoid Tissues of a Murine Food Allergy Model – M. Tsuda – International Archives of Allergy and Immunology

Disorder of gut amino acids metabolism during CKD progression is related with gut microbiota dysbiosis and metagenome change – Yang Liu – Journal of Pharmaceutical and Biomedical Analysis

Animal microbiome
The sponge microbiome project – Lucas Moitinho-Silva – Gigascience

Novel Microbial Diversity and Functional Potential in the Marine Mammal Oral Microbiome – Natasha K. Dudek – Current Biology

Review: Gut Brain Axis and Its Microbiota Regulation in Mammals and Birds – Jan S. Suchodolski- Veterinary Clinics of North America: Exotic Animal Practice

Analysis of Bacterial and Fungal Nucleic Acid in Canine Sterile Granulomatous and Pyogranulomatous Dermatitis and Panniculitis – Fabio B. Rosa – Veterinary Pathology

Developmental and gut-related changes to microbiomes of the cultured juvenile spiny lobster Panulirus ornatus – MC Ooi – FEMS Microbial Ecology
# Pubmed linked since DOI not yet active

Illumina Based Analysis of Bacterial and Fungal Flora in Foreguts and Hindguts of Crucian Carp (Carassius Aumtus) in Retail Markets – Mingyue Wang – Open Journal of Bacteriology

16S rRNA gene amplicon sequencing reveals dominance of Actinobacteria in Rhodnius pallescens compared to Triatoma maculata midgut microbiota in natural populations of vector insects from Colombia – Luisa M. Montoya-Porras – Acta Tropica

Plant, root, and soil microbiome
Exploration, antifungal and antiaflatoxigenic activity of halophilic bacteria communities from saline soils of Howze-Soltan playa in Iran – Samaneh Jafari – Extremophiles

No single driver of biodiversity: divergent responses of multiple taxa across land use types – Jamie R. Wood – Ecosphere

Community evolution increases plant productivity at low diversity – Sofia J. van Moorse – Ecology Letters

Co-Variation of Bacterial and Fungal Communities in Different Sorghum Cultivars and Growth Stages is Soil Dependent – Thiago R. Schlemper – Microbial Ecology

Microbial communities in the native habitats of Agaricus sinodeliciosus from Xinjiang Province revealed by amplicon sequencing – Jiemin Zhou – Scientific Reports

Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiome – Maria-Soledad Benitez – Scientific Reports

Soil bacterial community response to altered precipitation and temperature regimes in an old field grassland are mediated by plants – A Koyama – FEMS Microbial Ecology
# Pubmed linked since DOI not yet active

The abundance of health-associated bacteria is altered in PAH polluted soils-Implications for health in urban areas? – Anirudra Parajuli – PLoS One

Effect of halotolerant methylotrophs isolated from saline soil rhizosphere on diminution of salt stress in wheat (Triticum aestivum l.) – Dmitry Y. Sharavin – Journal of Agriculture and Environment

Build your own soil: exploring microfluidics to create microbial habitat structures – Kristin Aleklett – ISMEJ

Influence of high-carbon basal fertiliser on the structure and composition of a soil microbial community under tobacco cultivation – Song-tao Zhang – Research in Microbiology

Impacts of environmental factors on the whole microbial communities in the rhizosphere of a metal-tolerant plant: Elsholtzia haichowensis Sun – Songqiang Deng – Environmental Pollution

Contrasting the microbiomes from forest rhizosphere and deeper bulk soil from an Amazon rainforest reserve – Jose Pedro Fonseca – Gene

Microplot long-term experiment reveals strong soil type influence on bacteria composition and its functional diversity – Jarosław Grządziel – Applied Soil Ecology

Bulk soil bacterial community mediated by plant community in Mediterranean ecosystem, Israel – I. Moroenyane – Applied Soil Ecology
# From fellow MicrobiomeDigest contributor!

Thesis: Characterisation of Metagenomic Bougainvillea Soil DNA Through rDNA PCR Amplification – Aruna Ganesan – INTI International University

Book: Endophytes: Crop Productivity and Protection
Book chapter: Endophytes as Contender of Plant Productivity and Protection: An Introduction – Dinesh K. Maheshwari
Book chapter: Beneficial Effects of Bacterial Endophytes on Forest Tree Species – Akshit Puri

Water and extremophile microbiome
Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change – Julia Kleinteich – Frontiers in Ecology and Evolution

Microbial pathway for anaerobic 5′-methylthioadenosine metabolism coupled to ethylene formation – Justin A. North – PNAS

Built environment
Droplet distribution and airborne bacteria in an experimental shower unit – C.E. Estrada-Perez – Water Research

Mapping the ‘hospital microbiome’ and the spread of antimicrobial resistance and biofilm on the intensive care units from different regions – Khalid Johani – Infection, Disease, and Health

A study of microbial communities on terracotta separator and on biocathode of air breathing microbial fuel cells – Laura Rago – Bioelectrochemistry

Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes – Irena Maus – Biotechnology of Biofuels

Geochemical Influence on Microbial Communities at CO2-Leakage Analog Sites – Baknoon Ham – Frontiers in Microbiology (Extreme Microbiology)

Food microbiology
Evaluation of microbial consortia and chemical changes in spontaneous maize bran fermentation – Marilù Decimo – AMB Express

Novel insights into microbial community dynamics during the fermentation of Central European ice wine – Mária Bučková – International Journal of Food Microbiology

Probiotics / prebiotics / antibiotics
Treatment efficacy of a probiotic preparation for non-alcoholic steatohepatitis: a pilot trial – Elina Manzhalii – Journal of Digestive Diseases

Review: A Meta-Analysis of the Use of Probiotics to Alleviate Depressive Symptoms – Qin Xiang Ng – Journal of Affective Disorders

Review: Identification of probiotic effector molecules: present state and future perspectives – Sarah Lebeer – Current Opinion in Biotechnology

Review: Association between prior antibiotic therapy and subsequent risk of community-acquired infections: a systematic review – Umer Malik – Journal of Antimicrobial Therapy

Phages and viruses
The gut virome of the protochordate model organism, Ciona intestinalis subtype A – Brittany A. Leigh – Virus Research

Bioinformatics and statistical methods
Statistical analysis of co-occurrence patterns in microbial presence-absence datasets – Kumar P. Mainali – PLoS One

A Sequence-Based Mesh Classifier for the Prediction of Protein-Protein Interactions – Edgar D. Coelho – arXiv

Techniques
Analysis of single-cell genome sequences of bacteria and archaea – Robert M. Bowers – Emerging Topics in Life Sciences

A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites – John L. Chodkowski – mSystems

The inputs of metagenomics in the diagnostic of infectious diseases – G. Durand – Journal des Anti-infectieux

Genome announcements
Complete Genome Sequence of a Novel Nonnodulating Rhizobium Species Isolated from Agave americana L. Rhizosphere – Víctor Manuel Ruíz-Valdiviezo – genome Announcements

Complete Genome Sequence of Bacillus cereus C1L, a Plant Growth-Promoting Rhizobacterium from the Rhizosphere of Formosa Lily in Taiwan – Chien-Jui Huang – genome Announcements

Nocardia rhizosphaerihabitans sp. nov., a novel actinomycete isolated from a coastal soil – Peng Ding – International Journal of Systematic and Evolutionary Microbiology

The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics – Mohammad Bahram – PeerJ

*****************************
Microbes in the news
Gut bacteria at young age can contribute to MS disease onset and progression, study suggests – News Medical

Microbes on the market
Patent: Methods for distinguishing inflammatory bowel diseases using microbial community signatures – Wolfgang F. Fricke and James Robert White

Global Microbiome Sequencing Services Market Forecast to 2022 with Key Companies Profile, Supply, Demand, Cost Structure – Maciej Heyman – MilTech

Know about Microbiology Testing Market Posting +11% CAGR By 2022- Newly Invented Strategies, Healthcare Trends, Growth Opportunities, Forecast, & Key Players like Biomerieux S.A., Danaher, Becton, Dickinson and Company, Cepheid, Abbott, Alere, Bio-Rad Laboratories, Hologic, Bruker, F.Hoffmann-La Roche Ltd – MedGadget

November 18, 2017

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Featuring a bioinformatics paper from my former lab mate, as well as multiple, interesting pre-prints! See also a paper on rats in NYC and a study on peer review.

Events and jobs
Microbiology Technician I – Abbott – Plymouth, Minnesota, United States

Biology, Assistant Professor, Microbiology – College of Saint Benedict/Saint John’s University in Minnesota (3 year term, not tenure track)

PhD Studentship: Microbiome mediated resiliency of freshwater habitat – University of Birmingham

OMRF seeks participants as it launches new sarcoidosis clinic

General microbiome
Ecological Insights from the Evolutionary History of Microbial Innovations –
Mario E Muscarella – bioRxiv

Pregnancy and early life
Mode of delivery and child and adolescent psychological well-being: Evidence from Hong Kong’s “Children of 1997” birth cohort – Cherry Y. Leung – Scientific Reports

Multi-site human microbiome
Body size phenotypes comprehensively assess cardiometabolic risk and refine the association between obesity and gut microbiota – J de la Cuesta-Zuluaga – International Journal of Obesity

Human gut microbiome
Structural and functional differences in gut microbiome composition in patients undergoing haemodialysis or peritoneal dialysis – Vanessa Stadlbauer – Scientific Report

A role for bacterial urease in gut dysbiosis and Crohn’s disease – Josephine Ni – Science Translational Medicine

Animal experiments
Alteration of the intestinal microbiome characterizes preclinical inflammatory arthritis in mice and its modulation attenuates established arthritis – Rebecca Rogier – Scientific Reports

Dietary protein sources differentially affect microbiota, mTOR activity and transcription of mTOR signaling pathways in the small intestine – Soumya K. Kar – PLoS One

Blockade of CB1 cannabinoid receptor alters gut microbiota and attenuates inflammation and diet-induced obesity – Pegah Mehrpouya-Bahrami – Scientific Reports

Wild Microbiome Stems Tumorigenesis in Lab Mice – Cancer Discovery

Dietary chlorogenic acid regulates gut microbiota, serum-free amino acids and colonic serotonin levels in growing pigs – Yi Wu – International Journal of Food Sciences and Nutrition

Plant, root, and soil microbiomeSoil-mediated effects of global change on plant communities depend on plant growth form – Jes Hines – Ecosphere

Built environment
Spatial variation in the parasite communities and genomic structure of urban rats in New York City – L. P. Angley – Zoonoses and Public Health

Food microbiology
Digestion under saliva, simulated gastric and small intestinal conditions and fermentation in vitro of polysaccharides from the flowers of Camellia sinensis induced by human gut microbiota – Dan Chen – Food and Function

Review: Dietary and Endogenous Sphingolipid Metabolism in Chronic Inflammation – Gregory H. Norris – Nutrients

Review: Cardiovascular and Antiobesity Effects of Resveratrol Mediated through the Gut Microbiota – JK Bird – Advances in Nutrition

Review: Yogurt and Cardiometabolic Diseases: A Critical Review of Potential Mechanisms – MA Fernandez – Advances in Nutrition

Phages and viruses
Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics – Matthew T. Aliota – bioRxiv

Bioinformatics
A Bayesian method for detecting pairwise associations in compositional data – Emma Schwager – PLoS Computational Biology
Shout-out to my old lab mate, Emma!

MetQy: an R package to query metabolic functions of genes and genomes – Andrea Martinez-Vernon – bioRxiv

Genome announcements
Streptomyces tritici sp. nov., a novel actinomycete isolated from rhizosphere soil of wheat (Triticum aestivum L.) – Junwei Zhao – International Journal of Systematic and Evolutionary Biology

Rhodococcus psychrotolerans sp. nov., isolated from rhizosphere of Deschampsia antarctica – Leonardo Jose Silva – Antonie van Leeuwenhoek

Thalassotalea coralli sp. nov., isolated from the torch coral Euphyllia glabrescens – Der-Shyan Sheu – International Journal of Systematic and Evolutionary Biology

Microbes in the news
Lab-Grown Synthetic Nanobots May Officially End Antibiotic Resistance – Patrick Caughill – Futurism

Biolive yoghurt can help to lower blood pressure – Colin Fernandez – IOL

Dolphins: The final frontier for new types of bacteria? – Nicoletta Lanese – Scope

10 Things You Should Never Say to Someone With a Chronic Illness—Seriously – Karen Duffy – Health

Bacterium in a beetle makes it a leaf-eater – Science Daily
Paper: Drastic Genome Reduction in an Herbivore’s Pectinolytic Symbiont – Hassan Salem – Cell

How the Immune System Identifies Invading Bacteria – HHMI
Paper: The structural basis of flagellin detection by NAIP5: A strategy to limit pathogen immune evasion – Jeannette L. Tenthorey – Science

Dog owners have lower mortality, study finds – Katie Silver – BBC
No actual mention of microbiome in paper, which is: Dog ownership and the risk of cardiovascular disease and death – a nationwide cohort study – Mwenya Mubanga – Scientific Report

Microbes on the market
Evelo taps Mayo Clinic expertise for therapeutic bacteria programs – Phil Taylor – FierceBiotech

Human Microbiome Market Global Therapeutics, Drugs Review To 2025 – MedGadget

Researchers receive $500,000 grant to study the “microbiome of death” – Matt Wood – ScienceLife

Science, publishing, and career
Reviewer bias in single- versus double-blind peer review – Andrew Tomkins – PNAS