July 30, 2017

Relax into your Sunday and read through the days new microbiome research


Events and jobs

Laboratory Technician-Microbiology – Wilmington, DE

Pregnancy and early life

Maternal modifiers of the infant gut microbiota: metabolic consequences – Christopher M Mulligan – Journal of Endocrinology

Human respiratory microbiome

Composition and abundance of microbiota in the pharynx in patients with laryngeal carcinoma and vocal cord polyps – Hongli Gong – Journal of Microbiology

Human gut microbiome

Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis – Chengping Wen – Genome Biology

Persistent diarrhea: A persistent infection with enteropathogens or a gut commensal dysbiosis? – Shafiqul A. Sarker – Environmental Microbiology

Reproducibility of assessing fecal microbiota in chronic constipation – G. Parthasarathy – Neurogastroenterology & Motility

Effects of mushroom consumption on the microbiota of different target groups – Impact of polyphenolic composition and mitigation on the microbiome fingerprint – Emanuel Vamanu – LWT – Food Science and Technology

Shotgun metagenomic data on the human stool samples to characterize shifts of the gut microbial profile after the Helicobacter pylori eradication therapy – Eugenia A. Boulygina – Data in Brief

Review: Strategies to increase the efficacy of using gut microbiota for the modulation of obesity – J. Li – Obesity Reviews

Animal experiments 

Amino acid metabolic signaling influences Aedes aegypti midgut microbiome variability – Sarah M. Short – PLOS One

Differential intestinal anti-inflammatory effects of Lactobacillus fermentum and Lactobacillus salivarius in DSS mouse colitis: impact on microRNAs expression and microbiota composition – Alba Rodríguez-Nogales – Molecular Nutrition & Food Research

Animal microbiome

Links between Natural Variation in the Microbiome and Host Fitness in Wild Mammals – Taichi A. Suzuki – Integrative and Comparative Biology

Captivity Shapes the Gut Microbiota of Andean Bears: Insights into Health Surveillance – Andrea Borbón-García – Frontiers in Microbiology

Microbiomes of American Oysters (Crassostrea virginica) Harvested from Two Sites in the Chesapeake Bay – Sylvia Ossai – Genome Announcements

Rumen Microbiome, Probiotics, and Fermentation Additives – Joshua C. McCann – Veterinary Clinics of North America: Food Animal Practice

Plant, root, and soil microbiome

Assessing the influence of farm fertility amendments, field management, and sorghum genotypes on soil microbial communities and grain quality – Adam B. Cobb – Applied Soil Ecology

Rhizospheric Microbiome Profiling of Capsicum annuum L. Cultivated in Amended Soils by 16S and Internal Transcribed Spacer 2 rRNA Amplicon Metagenome Sequencing – Ali Asaff-Torres – Genome Announcements

Peaks of in situ N2O emissions are influenced by N2O producing and reducing microbial communities across arable soils – L.A Domeignoz-Horta – Global Change Biology

Eelgrass Leaf Surface Microbiomes Are Locally Variable and Highly Correlated with Epibiotic Eukaryotes – Mia M. Bengtsson – Frontiers in Microbiology

Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage – A.J. Ashworth – Soil Biology and Biochemistry

Interaction of microorganisms within leafy green phyllospheres: Where do human noroviruses fit in? – Wenjun Deng – International Journal of Food Microbiology

Water and extremophile microbiome

Spatial and Temporal Microbial Patterns in a Tropical Macrotidal Estuary Subject to Urbanization – Mirjam Kaestli – Frontiers in Microbiology

Evidence of microbial rhodopsins in Antarctic Dry Valley edaphic systems – Leandro D. Guerrero – Environmental Microbiology

Prokaryotic diversity and community composition in the Salar de Uyuni, a large scale, chaotropic salt flat – Sergio S. Rubin – Environmental Microbiology

Fate of antibiotic resistance genes and their associations with bacterial community in livestock breeding wastewater and its receiving river water – Shuyu Jia – Water Research

Performance and microbial community analysis of a microaerophilic sulfate and nitrate co-reduction system – Xi-Jun Xu – Chemical Engineering Journal

Characteristics of microbial community functional structure of a biological coking wastewater treatment system – Dev Raj Joshi – Journal of Environmental Sciences

Food microbiology

Evolution of microbial community and chemical properties of a sourdough during the production of Colomba, an Italian sweet leavened baked product – Stefano Raimondi – LWT – Food Science and Technology

Bacterial community diversity of traditional fermented vegetables in China – Daqun Liu – LWT – Food Science and Technology

July 15, 2017

Enjoy your weekend with Saturdays microbiome digest. Lots of animal microbiome research out today, plus several human microbiome reviews and infant microbiome research.

Events and jobs

Molecular Scientist – Phage Display – Cambridge, UK

Research Officer Microbiology – Western Sydney, AUS

Research Assistant – Microbiology & Immunology – Illinois, USA

Medical Laboratory Scientist – Microbiology – Dunedin, New Zealand

General microbiome

Eco-Aging: stem cells and microbes are controlled by aging antagonist FoxO – Benedikt M Mortzfeld – Current Opinion in Microbiology

Gut–CNS-Axis as Possibility to Modulate Inflammatory Disease Activity—Implications for Multiple Sclerosis – Ann-Katrin Fleck – International Journal of Molecular Sciences

Pregnancy and early life

Early intervention with Bifidobacterium lactis NCC2818 modulates the host-microbe interface independent of the sustained changes induced by the neonatal environment – Marie C. Lewis – Scientific Reports

Virulence and Antibiotic Resistance of Enterococci Isolated from Healthy Breastfed Infants – Landete José M – Microbial Drug Resistance

Association of Antibiotics, Airway Microbiome and Inflammation in Infants with Cystic Fibrosis – Jessica E Pittman – Annals of the American Thoracic Society

Nasopharyngeal microbiota in infants and changes during viral upper respiratory tract infection and acute otitis media – Tasnee Chonmaitree – PLOS One

Human respiratory microbiome

A reproducible microcosm biofilm model of subgingival microbial communities – M. Fernandez y Mostajo – Journal of Periodontal Research

Review – Microbiome in chronic obstructive pulmonary disease – Eduard Monsó – Annals of Translational Medicine

Review – More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes – Kees C. H – Microbiome

Review – The respiratory microbiome in idiopathic pulmonary fibrosis – Richard J. Hewitt – Annals of Translational Medicine

Human skin microbiome

Review – Cleanliness in context: reconciling hygiene with a modern microbial perspective – Roo Vandegrift – Microbiome

Human gut microbiome

High frequency of intestinal TH17 cells correlates with microbiota alterations and disease activity in multiple sclerosis – Ilaria Cosorich – Science Advances

Systematic review with meta-analysis: the efficacy of faecal microbiota transplantation for the treatment of recurrent and refractory Clostridium difficile infection – M. N. Quraishi – Alimentary Pharmacology & Therapeutics

Animal experiments 

Preprint – Disentangling metabolic functions of bacteria in the honey bee gut – Lucie Kesnerova – BioRxiv

Prion disease pathogenesis in the absence of the commensal microbiota – Barry M. Bradford – Journal of General Virology

A bidirectional association between the gut microbiota and CNS disease in a biphasic murine model of multiple sclerosis – Sara L. Colpitts – Gut Microbes

Effects of Consuming Xylitol on Gut Microbiota and Lipid Metabolism in Mice – Takashi Uebanso – Nutrients

Polydextrose changes the gut microbiome and attenuates fasting triglyceride and cholesterol levels in Western diet fed mice – Ghulam Shere Raza – Scientific Reports

Formula diet driven microbiota shifts tryptophan metabolism from serotonin to tryptamine in neonatal porcine colon – Manish Kumar Saraf – Microbiome

Regulation by gut bacteria of immune response, Bacillus thuringiensis susceptibility and hemolin expression in Plodia interpunctella – Alonso A.Orozco-Flores – Journal of Insect Physiology

Plant, root, and soil microbiome

Dynamics of culturable mesophilic bacterial communities of three fresh herbs and their production environment – Maria-Theresia Gekenidis – Journal of Applied Microbiology


Review – Insights into study design and statistical analyses in translational microbiome studies – Jyoti Shankar – Annals of Translational Medicine


Assessing the impact of protein extraction methods for human gut metaproteomics – Xu Zhang – Journal of Proteomics

Microbes in the news

Micromotors are powered by bacteria, controlled by light  – Lisa Zyga – Phys.org

July 9, 2017

Double Day Digest! Today we have picks for the entire weekend in one post, so here is a great selection!


Events and jobs

Laboratory Technician – Cranleigh Scientific – Cambridge, England

General microbiome

Review – Food-animal production and the spread of antibiotic resistance: the role of ecology – Benjamin J Koch – Frontiers in Ecology and the Enviroment

Human skin microbiome 

Impact of coated TiO2-nanoparticles used in sunscreens on two representative strains of the human microbiota: Effect of the particle surface nature and aging – Laura Rowenczyk – Colloids and Surfaces B: Biointerfaces

Human gut microbiome

Review – Gut microbiome, metabolome, and allergic diseases – So-ichiro Hirata – Allergology International

Review – Bile Acids and Intestinal Microbiota in Autoimmune Cholestatic Liver Diseases – You Li – Autoimmunity Reviews

Bifidobacterium animalis subsp. lactis LKM512 reduces levels of intestinal trimethylamine produced by intestinal microbiota in healthy volunteers: A double-blind, placebo-controlled study – Mitsuharu Matsumoto – Journal of Functional Foods

Animal experiments

Long-term consumption of caffeine-free high sucrose cola beverages aggravates the pathogenesis of EAE in mice – Guangchao Cao  – Cell Discovery

Review – Using probiotics to improve swine gut health and nutrient utilization – Shengfa F. Liao – Animal Nutrition

Dietary and lifestyle disease indices and caecal microbiota in high fat diet, dietary fibre free diet, or DSS induced IBD models in ICR mice – Takashi Kuda – Journal of Functional Foods

Head-injury profoundly affects gut microbiota homeostasis: results of a pilot study – Anne-Judith Waligora-Dupriet – Nutrition

Animal microbiome

Review – Marine animal microbiomes: towards understanding host-microbiome interactions in a changing ocean – Amy Apprill – Frontiers in Marine Science

Influence of elevation in structuring the gut bacterial communities of Apis cerana – S Sudhagar – Journal of Entomology and Zoology Studies

Plant, root, and soil microbiome

Comparison of soil biosolarization with mesophilic and thermophilic solid digestates on soil microbial quantity and diversity – Jesús D. Fernández-Bayo – Applied Soil Ecology

Contrasting habitats but comparable microbial decomposition in the benthic and hyporheic zone – Ute Risse-Buhl – Science of The Total Environment

Beneficial traits of bacterial endophytes belonging to the core communities of the tomato root microbiome – Baoyu Tian – Agriculture, Ecosystems & Environment

Long- term grapevine cultivation and agro-environment affect rhizosphere microbiome rather than plant age – L.M. Manici – Applied Soil Ecology

Comparison of soil biosolarization with mesophilic and thermophilic solid digestates on soil microbial quantity and diversity – Jesús D. Fernández-Bayo – Applied Soil Ecology

Positive effects of plant association on rhizosphere microbial communities depend on plant species involved and soil nitrogen level – Barbara Pivato – Soil Biology and Biochemistry

Water and extremophile microbiome

Current Trend of Metagenomic Data Analytics for Cyanobacteria Blooms – JianDong Huang – Journal of Geoscience and Environment Protection

Early bacterial biofilm colonizers in the coastal waters of Mauritius – Sillma Rampadarath – Electronic Journal of Biotechnology

Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements – Jianhua Guo – Water Research

Characterization of microbial signatures from advanced treated wastewater biofilms – Leddy, Menu B – AMERICAN WATER WORKS ASSOCIATION

Greater diversity of soil fungal communities and distinguishable seasonal variation in temperate deciduous forests compared with subtropical evergreen forests of eastern China – Jinhong He – FEMS Microbiology Ecology

Microbes from mined sites: Harnessing their potential for reclamation of derelict mine sites – Palanisami Thavamani – Environmental Pollution

Bacterial communities and chemical parameters in soils and coastal sediments in response to diesel spills at Carlini Station, Antarctica – Susana Vázquez – Science of The Total Environment

Food microbiology

Elucidating microbial community adaptation to anaerobic co-digestion of fats, oils, and grease and food waste – Yamrot M. Amha – Water Research


Personalized microbiome dynamics – Cytometric fingerprints for routine diagnostics – Christin Koch – Molecular Aspects of Medicine

Development of a real-time PCR method for quantification of Prevotella histicola from the gut – Baskar Balakrishnan – Anaerobe

Microbes in the news

Why Life on Mars May Be Impossible – TIME – Jeffrey Kluger

June 18, 2017

Quite a large Digest for a Sunday, with most picks being on soil microbiome and some interesting animal papers including how microbial genetic composition may tune host longevity (Bing Han – Cell)

General microbiome

Reply to Wang and Chen: An ancient origin of magnetotactic bacteria – Wei Lin – Proceedings of the National Academy of Sciences of the United States of America

Microbiome and Longevity: Gut Microbes Send Signals to Host Mitochondria – Jan Gruber – Cell

Human gut microbiome

The Human Microbiome and the Missing Heritability Problem – Santiago Sandoval-Motta – Frontiers in Genetics

Bacteriophages important for FMT efficacy – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Postmortem succession of gut microbial communities in deceased human subjects – Jennifer M. DeBruyn – Peerj

Urinary metabolic insights into host-gut microbial interactions in healthy and IBD children – Francois-Pierre Martin – World Journal of Gastroenterology

Animal experiments

Profound perturbation induced by triclosan exposure in mouse gut microbiome: a less resilient microbial community with elevated antibiotic and metal resistomes – Bei Gao – BMC Pharmacology and Toxicology

Vitamin A deficiency in mice results in a hypermetabolic state, dysbiosis and alterations in bacterial metabolism – Yuan Tian – The Journal of Immunology

Host–microbiota interactions in Caenorhabditis elegans and their significance – Michael Shapira – Current Opinion in Microbiology

Microbial Genetic Composition Tunes Host Longevity – Bing Han – Cell

Probabilistic Invasion Underlies Natural Gut Microbiome Stability – Benjamin Obadia – Current Biology

Animal microbiome

Metagenomic survey of bacteria associated with the invasive ladybird Harmonia axyridis (Coleoptera: Coccinellidae) – Krzysztof Dudek – European Journal of Entomology

Plant, root, and soil microbiome

Microbial mechanisms controlling the rhizosphere effect of ryegrass on degradation of polycyclic aromatic hydrocarbons in an aged-contaminated agricultural soil – Meixia Guo – Soil Biology and Biochemistry

Illumina-Based Analysis of Bulk and Rhizosphere Soil Bacterial Communities in Paddy Fields Under Mixed Heavy Metal Contamination – HE Huaidong  – Pedosphere

Paracoccus hibisci sp. nov., isolated from the rhizosphere of Hibiscus syriacus L. (Mugunghwa flower) – Zheng-Fei Yan – International Journal of Systematic and Evolutionary Microbiology

The role of Plant Growth Promoting Bacteria in improving nitrogen use efficiency for sustainable crop production: a focus on wheat – Nilde Antonella Di Benedetto – AIMS Microbiology Special Issue: Plant probiotic bacteria: solutions to feed the World

Molecular Communication and Nutrient Transfer of Arbuscular Mycorrhizal Fungi, Symbiotic Nitrogen-Fixing Bacteria, and Host Plant in Tripartite Symbiosis – Chunling Chang – Legume Nitrogen Fixation in Soils with Low Phosphorus Availability

Experimental study on the effects of underground CO2 leakage on soil microbial consortia – Fu Chen – International Journal of Greenhouse Gas Control

The Impact of Hydration and Temperature on Bacterial Diversity in Arid Soil Mesocosms – Adam Št’ovíček – Frontiers in Microbiology

In vitro and in silico characterization of metagenomic soil-derived cellulases capable of hydrolyzing oil palm empty fruit bunch – Laura Marcela Palma Medina – Biotechnology Reports

The impacts of organic amendments: Do they confer stability against drought on the soil microbial community? – F. Bastida – Soil Biology and Biochemistry


Review: Harnessing Whole Genome Sequencing in Medical Mycology – Christina A Cuomo – Current Fungal Infection Reports

From complex gut communities to minimal microbiomes via cultivation – Thomas Clavel – Current Opinion in Microbiology

Microbes in the news

Microbiome ‘fingerprint’ shows donor microbes persist in fecal transplant recipients –R Kumar – Healio Gastroenterology

New Pasteurization Alternative Sanitizes Milk Without Killing Good Bacteria – Luke Dormehl – Digitaltrends

Gut Bacteria May Help Slow Down Process of Ageing – NDTV

Gut microbiota – Tiny helpers against Samonella – Innovations-report

11 June, 2017

Events and jobs

Doctoral researcher in Microbiology/Virology – Helmholtz Centre for Environmental Research – UFZ – Germany

General microbiome

Review: Role of Gut Microbiota in Rheumatoid Arthritis – Y. Maeda – Journal of Clinical Medicine
Review: The Mycobiome: Impact on Health and Disease States –  N. El-Jurdi – Microbiology Spectrum

Pregnancy and early life

Review: Early-Life Host–Microbiome Interphase: The Key Frontier for Immune Development – N. Amenyogbe – Frontiers in Pediatrics

Human skin microbiome

Temporal Dynamics Of Relative Abundances And Bacterial Succession In Chronic Wound Communities – C.D. Tipton – Wound Repair and Regeneration

Human vaginal microbiome

Therapeutic Opportunities in the Vaginal Microbiome – G. Reid – Microbiology Spectrum

Human gut microbiome

Review: Microbial Impact on Host Metabolism: Opportunities for Novel Treatments of Nutritional Disorders? – H. Plovier – Microbiology Spectrum
Nickel-resistant bacteria isolated in human microbiome – E.A. Lusi – New Microbes and New Infections

Animal experiments

Keratin 8 reduces colonic permeability and maintains gut microbiota homeostasis, protecting against colitis and colitisassociated tumorigenesis – C. Liu – Oncotarget
Evolution of commensal bacteria in the intestinal tract of mice – A. Sousa – Current Opinion in Microbiology

Animal microbiome

Gut Microbiota Dysbiosis in Postweaning Piglets: Understanding the Keys to Health – R. Gresse – Trends in Microbiology
Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome – S.M. Wolff – Microbiome

Plant, root, and soil microbiome

Community analysis of Persian oak fungal microbiome under dust storm conditions – N.H. Doust – Fungal Ecology
Maternal effects on phenotype, resistance and the structuring of fungal communities in Eucalyptus grandis – M. Vivas – Environmental and Experimental Botany
Review: Iron and Immunity – E.H. Verbon – Annual Review of Phytopathology
Dispersal enhances beta diversity in nectar microbes – R.L. Vannette – Ecology Letters

Water and extremophile microbiome

Application of long amplicon propidium monoazide-PCR to assess the effects of temperature and background microbiota on pathogens in river water – A. Banihashemi – Journal of Water and Health

Microbes in the news

Gut bacteria can stop cancer drugs from working – S. Reardon – Nature News
Fungi revive starving bacteria – K. Evans – Labroots
Did the microbiome help drive human evolution? – S.E. Erdman – STAT news

June 5, 2017

Microbiology today

We have a group of nice articles on careers in microbiology and chance to view  “Women in Microbiology – Esther Lederberg” a live session from Microbe 2017. Science articles today include Predictors of phenotypic switching in bacteria, Determinants of bone mass regulation by the gut microbiota (in mice), and Phylogenetic and functional diversity of bacteria in soils.

Events and jobs

Microbiology Associate – CryoLife Inc – Kennesaw, GA

General microbiome

Preprint: Dynamical predictors of an imminent phenotypic switch in bacteria – H. Wang – BioRxiv

Preprint: Metabolic changes of the host-pathogen environment in a Cryptosporidium infection – C. Miller – BioRxiv

Human respiratory microbiome

The microbial changes in subgingival plaques of orthodontic patients: a systematic review and meta-analysis of clinical trials – R. Guo – BMC Oral Health

The lung microbiota (in French) – M. Ploton – Archives de Pédiatrie

Human gut microbiome

Review: Gut microbiota and acute graft-versus-host disease – K. Yoshioka – Pharmacological Research

Animal experiments

Preprint: Chondroitin Sulfate Flourishes Gut Sulfatase-Secreting Bacteria To Damage Mucus Layers, Leak Bacterial Debris, And Trigger Inflammatory Lesions In Mice – T. Liao – BioRxiv

Regulation of bone mass by the gut microbiota is dependent on NOD1 and NOD2 signaling – C. Ohlsson – Cellular Immunology

Plant, root, and soil microbiome

Phylogenetic and functional diversity of total (DNA) and expressed (RNA) bacterial communities in urban green infrastructure bioswale soils – A. Gill – Applied and Environmental Microbiology

Microbes in the news

Enhanced test for urinary tract infections detects more bacteria than standard test – MedicalXpress

Vaginal Bacteria Alter Sexual Transmission Of Zika And Herpes Simplex Virus-2 – ASM Press Release

Science, publishing, and career

Women In Microbiology – Esther Lederberg – Chris Condayan – ASM

Careers In Microbiology – An Insiders’ Guide To Finding A Job – Chris Condayan – ASM

Microbiology Careers: Which One Is Right For You? – Chris Condayan – ASM

May 14, 2017

A short digest this Sunday with most studies focusing on associations with microbiota and host health, plus a look at a novel sampling method for assessing human-pathogen interactions.


 General microbiome

Review: Using systems biology approaches to elucidate cause and effect in host-microbiome interactions – Elizabeth A. Witherden – Current Opinion in Systems Biology

Human gut microbiome

Dynamic gastrointestinal digestion of grape pomace extracts: bioaccessible phenolic metabolites and impact on human gut microbiota – Irene Gil-Sánchez – Journal of Food Composition and Analysis

Gut Microbiota in Parkinson Disease in a northern German cohort – Franziska Hopfner – Brain Research

Outlier based literature exploration for cross-domain linking of Alzheimer’s disease and gut microbiota – Donatella Gubiani – Expert Systems with Applications

Animal experiments

Review: This Gut Ain’t Big Enough for Both of Us. Or Is It? Helminth–Microbiota Interactions in Veterinary Species – Laura E. Peachey – Trends in Parasitology

Lactobacillus johnsonii CJLJ103 attenuates colitis and memory impairment in mice by inhibiting gut microbiota lipopolysaccharide production and NF-κB activation – Su-Min Lim – Journal of Functional Foods

Effects of potato dextrin on the composition and metabolism of the gut microbiota in rats fed standard and high-fat diets – Renata Barczynska – Journal of Functional Foods

Antibiotics-induced gut microbiota dysbiosis promotes tumor initiation via affecting APC-Th1 development in mice – Chengming Xu – Biochemical and Biophysical Research Communications

Plant, root, and soil microbiome

Effectiveness of a full-scale horizontal slow sand filter for controlling phytopathogens in recirculating hydroponics: From microbial isolation to full microbiome assessment – Francesc X. Prenafeta-Boldú – Science of The Total Environment

Functioning grouped soil microbial communities according to ecosystem type, based on comparison of fallows and meadows in the same region – Dominika Chmolowska – Science of The Total Environment

Effect of fumigation with chloropicrin on soil bacterial communities and genes encoding key enzymes involved in nitrogen cycling – Jun Li – Environmental Pollution


A novel sampling method for assessing human-pathogen interactions in the natural environment using boot socks and citizen scientists, with an application to the seasonality of Campylobacter – Natalia R Jones – Applied and Environmental Microbiology

Microbes in the news

The Coral Microbiome May Offer Protection in Warming Seas – Jeffrey Marlow – Discover

Grotty socks reveal surprising spread of gut-churning bacteria – Ben Guarino – Stuff

UK researchers develop low tech method for environmental sampling of campylobacter – ASM Press release