November 19, 2017

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

ReviewLipotoxicity and the gut-liver axis in NASH pathogenesis – Fabio Marra – Journal of Hepatology

ReviewEvidence 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 chapterEndophytes as Contender of Plant Productivity and Protection: An Introduction – Dinesh K. Maheshwari
Book chapterBeneficial 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

ReviewA 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

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

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

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

November 17, 2017

Jobs and events

Lab Assistant – Microbiology, Dublin Ohio

General microbiome

Evolution of the hygiene hypothesis into biota alteration theory: what are the paradigms and where are the clinical applications? – Chantal Villeneuve, Microbes and Infection

Human gut microbiome

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

Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks – Anubhav Das, Scientific Reports

Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut – Natalya Yutin, Nature Microbiology

Fecal Transplantation for Treatment of Clostridium Difficile Infection in Elderly and Debilitated Patients – Tali Friedman-Korn, Digestive Diseases and Sciences

Myocardial infarction and gut microbiota: an incidental connection – Sepideh ZununiVahed, Pharmacological Research

Anxiety, Depression, and the Microbiome: A Role for Gut Peptides – Gilliard Lach, Neurotherapeutics

The nursing home elder microbiome stability and associations with age, frailty, nutrition and physical location – John P. Haran, Journal of Medical Microbiology

Human nearly-sterile sites

Risk of Subsequent Sepsis within 90 Days of a Previous Hospital Stay by Type of Antibiotic Exposure – James Baggs, Clinical Infectious Diseases

Human vaginal microbiome

Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women – Supriya D. Mehta, Scientific Reports

Animal experiments

The green tea modulates large intestinal microbiome and exo/endogenous metabolome altered through chronic UVB-exposure – Eun Sung Jung, PLOS ONE

Acute Administration of the Nonpathogenic, Saprophytic Bacterium, Mycobacterium vaccae, Induces Activation of Serotonergic Neurons in the Dorsal Raphe Nucleus and Antidepressant-Like Behavior in Association with Mild Hypothermia – Philip H. Siebler, Cellular and Molecular Neurobiology

Maternal High Fat Diet and its Consequence on the Gut Microbiome: A Rat Model – Phyllis E. Mann, Gut Microbes

Environmental Burkholderia cenocepacia Strain Enhances Fitness by Serial Passages during Long-Term Chronic Airways Infection in Mice – Alessandra Bragonzi, International Journal of Molecular Sciences

Enteric Delivery of Regenerating Family Member 3 alpha Alters the Intestinal Microbiota and Controls Inflammation in Mice With Colitis – Marion Darnaud, Gastroenterology

Animal microbiome

Novel viruses in salivary glands of mosquitoes from sylvatic Cerrado, Midwestern Brazil – Andressa Zelenski de Lara Pinto, PLOS ONE

New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection – Jiang Hong Li, PLOS ONE

Relative importance of honeydew and resin for the microbial activity in wood ant nest and forest floor substrate – a laboratory study – Veronika Jílková, Soil Biology and Biochemistry

Common Cutaneous Bacteria Isolated from Snakes Inhibit Growth of Ophidiomyces ophiodiicola – Aubree J. Hill, EcoHealth

Plant, root, and soil microbiome

Fungal community reveals less dispersal limitation and potentially more connected network than that of bacteria in bamboo forest soils – Xian Xiao, Molecular Ecology

Influence of compost and biochar on microbial communities and the sorption/degradation of PAHs and NSO-substituted PAHs in contaminated soils – Gabriel Sigmund, Journal of Hazardous Materials

Epiphytic Bacteria Alter Floral Scent Emissions – Carola Helletsgruber, Journal of Chemical Ecology

In vitro bacterization of banana (Musa spp.) with native endophytic and rhizospheric bacterial isolates: Novel ways to combat Fusarium wilt – M. Kavino, European Journal of Plant Pathology

Foliar microbiome transplants confer disease resistance in a critically-endangered plant – Geoffrey Zahn, PeerJ

The response of soil microbial communities to variation in annual precipitation depends on soil nutritional status in an oligotrophic desert – Cristina Montiel-González, PeerJ

Entomopathogenic Fungi as Dual Control Agents against Both the Pest Myzus persicae and Phytopathogen Botrytis cinerea – Hwi-Geon Yun, Mycobiology

Glycomyces rhizosphaerae sp. nov., isolated from the root and rhizosphere soil of wheat (Triticum aestivum L.) – Wenchao Li, International Journal of Systematic and Evolutionary Microbiology

Water and extremophile microbiome

A comparison between biostimulation and bioaugmentation in a solid treatment of anaerobic sludge: Drug content and microbial evaluation – G. Llorens-Blanch, Waste Management

Iron Chloride Flocculation of Bacteriophages from Seawater – Bonnie T. Poulos, Bacteriophages

Multi-Level Contact Oxidation Process Performance When Treating Automobile Painting Wastewater: Pollutant Removal Efficiency and Microbial Community Structures – Yufang Zhu, Water

Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments – Brodie Sutcliffe, Microbial Ecology

Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization? – Dave R. Clark, Global Ecology and Biogeography

Diversity of microbiota found in coffee processing wastewater treatment plant – Josiane Ferreira Pires, World Journal of Microbiology and Biotechnology

Food microbiology

Epiphytic fungal community in Vitis vinifera of the Portuguese wine regions – M. Oliveira, Letters in Applied Microbiology


HgtSIM: a simulator for horizontal gene transfer (HGT) in microbial communities – Weizhi Song, PeerJ


Significance estimation for large scale metabolomics annotations by spectral matching – Kerstin Scheubert, Nature

Single primer isothermal amplification (SPIA) combined with next generation sequencing provides complete bovine coronavirus genome coverage and higher sequence depth compared to sequence-independent single primer amplification (SISPA) – Mette Myrmel, PLOS ONE

Developing selective media for quantification of multispecies biofilms following antibiotic treatment – Eva Vandeplassche, PLOS ONE

Microbes in the news

Microbiology: Bacteria disarm host-defence proteins – John D. MacMicking, Nature News and Views

Probiotics: Health boost or waste of cash? – Anne Allred, 5-ON-YOUR-SIDE

Cygnus Open for Business; Crew Unloading New Bacteria, Plant and Tech Studies – Mark Garcia, NASA blog

Bacteria Hysteria

Your supermarket is filled with germs — here are 7 facts that will make you dread grocery shopping –  Joanna Fantozzi, Insider

November 16, 2017

Today we have a very nice serving to digest, with some impactful gut microbiome studies for human health/therapeutics, a whitepaper on the challenges of clinical microbiome research.  We also have clusters of related studies on the environment, drinking water, and antibiotic resistance.  There are even a few studies on the microbiota found in caves!  Give these all a read, there is a lot of amazing research today.  Don’t forget to have yourself a few extra side servings of my own non-microbial picks, in honor of the upcoming Thanksgiving US holiday.

Human oral microbiome

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation – Koji Atarashi – Science

Human respiratory microbiome

The microbiota protects against respiratory infection via GM-CSF signaling – Rebecca L. Brown – Nature

Human gut microbiome

Microbiota: A high-pressure situation for bacteria – David A. Relman – Nature

Quantitative microbiome profiling links gut community variation to microbial load – Doris Vandeputte – Nature

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

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

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

New evidence showing that the destruction of gut bacteria by antibiotic treatment could increase the honey bee’s vulnerability to Nosema infection – Jiang Hong Li – PLOS ONE

Plant, root, and soil microbiome

[Doctoral Thesis] Plant biomass-degrading microbial consortia: Ecology, lignocellulolytic machinery and biotechnological potential – Jiménez Avella – University of Groningen

Direct evidence for the enhanced acquisition of phosphorus in the rhizosphere of aquatic plants: A case study on Vallisneria natans – Xigang Xing – Science of the Total Environment

Effect of Phosphate Solubilization Microorganisms and Plant Growth Promoting Rhizobacteria on Yield and Yield Components of Corn – Amin Fathi – Scientia Agriculturae

Water and extremophile microbiome

Diverse Marinimicrobia bacteria may mediate coupled biogeochemical cycles along eco-thermodynamic gradients – Alyse K. Hawley – Nature

Comparison of bacterial and archaeal communities from different habitats of the hypogenic Molnár János Cave of the Buda Thermal Karst System (Hungary) – Dóra Anda – Journal of Cave and Karst Studies

Comparisons of Soil Properties, Enzyme Activities and Microbial Communities in Heavy Metal Contaminated Bulk and Rhizosphere Soils of Robinia pseudoacacia L. in the Northern Foot of Qinling Mountain – Yurong Yang – Forests

Biofilm biodiversity in French and Swiss show caves using the metabarcoding approach: First data – Stéphane Pfendler – Science of the Total Environment

Amoxicillin effects on functional microbial community and spread of antibiotic resistance genes in amoxicillin manufacture wastewater treatment system – Lingwei Meng – Journal of Environmental Sciences

Field assessment of bacterial communities and total trihalomethanes: Implications for drinking water networks – Carolina Montoya-Pachongo – Science of the Total Environment

Persistence of antibiotic resistance genes and bacterial community changes in drinking water treatment system: From drinking water source to tap water – Hao-Chang Su –  Science of the Total Environment


Phylogenic inference using alignment-free methods for applications in microbial community surveys using 16s rRNA gene – Yifei Zhang – PLOS ONE

Microbes in the news

Probiotics: Health boost or waste of cash?

Microbes on the market

* uBiome Launches HPV, STD, Vaginal Microbiome Test for Self-Collected Samples – genomeweb

* [Whitepaper] The Microbiome in Clinical Trials: Opportunities and Challenges – Brian Murphy – MedPace

Bacteria Hysteria

Fort Mitchell woman attacked by flesh-eating bacteria back home after 45 days in hospital

Fecal Bacteria Discovered In Public Well Serving Seymour, Oxford

Ed’s non-microbiology picks

Epistemic rationality: Skepticism toward unfounded beliefs requires sufficient cognitive ability and motivation to be rational – Tomas Ståhl – Personality and Individual Differences

Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing – Hao Yin – Nature

Increased food production and reduced water use through optimized crop distribution – Kyle Frankel Davis – Nature Geoscience

* Fructan, Rather Than Gluten, Induces Symptoms in Patients With Self-reported Non-celiac Gluten Sensitivity – Gry I. Skodje – Gastroenterology

* Does Money Matter in the Long Run? Effects of School Spending on Educational Attainment – Joshua Hyman – American Economy Journal: Economic Policy

* Hippocampal GABA enables inhibitory control over unwanted thoughts – Taylor W. Schmitz – Nature

Daytime variation of perioperative myocardial injury in cardiac surgery and its prevention by Rev-Erbα antagonism: a single-centre propensity-matched cohort study and a randomised study – David Montaigne – The Lancet Cardiac Surgery

The reminiscence bump: why America’s greatest year was probably when you were young

Study: Americans are retiring later, dying sooner and sicker in-between

November 15, 2017

Virome analysis of bats and archaea, bioinformatics tools for metatranscriptomics analysis, using mass spectrometry for studying microbiome metabolomics.

General microbiome

Review: An integrative omics perspective for the analysis of chemical signals in ecological interactions – A E Brunetti – Chemical Society Reviews

Pregnancy and early life

Pre-print: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T Brown – bioRxiv

Human respiratory microbiome

The role of the microbiome in childhood asthma – Giovanna Pisi – Immunotherapy

Human vaginal microbiome

Pre-print: A new sequencing-based women’s health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis – Elisabeth M Bik – bioRxiv

Human gut microbiome

Gut microbiota and body composition in anorexia nervosa inpatients in comparison to athletes, overweight, obese, and normal weight controls – Sabrina Mörkl – International Journal of Eating Disorders

Review: Gut Microbiota-Dependent Modulation of Energy Metabolism – C N Heiss – Journal of Innate Immunity

Animal experiments

Antimicrobial emulsifier – glycerol monolaurate induces metabolic syndrome, gut microbiota dysbiosis and systemic low-grade inflammation in low-fat diet fed mice – Zengliang Jiang – Molecular Nutrition and Food Research

A temperature sensitive Mycobacterium paragordonae induces enhanced protective immune responses against mycobacterial infections in the mouse model – Byoung-Jun Kim – Scientific Reports

Animal microbiome

Review: The B vitamin nutrition of insects: the contributions of diet, microbiome and horizontally acquired genes – Angela E Douglas – Current Opinion in Insect Science

Plant, root, and soil microbiome

Brassica napus has a key role in the recovery of the health of soils contaminated with metals and diesel by rhizoremediation – Rafael G Lacalle – Science of the Total Environment

Water and extremophile microbiome

Purification of eutrophic water containing chlorpyrifos by aquatic plants and its effects on planktonic bacteria – Xing-Jian Xu – Chemosphere

Cultivation of an immobilized (hyper)thermophilic marine microbial community in a bioreactor – M Landreau – FEMS Microbiology Letters

Pre-print: Dynamics of finely resolved, abundant symbiotic marine plankton and other interacting microbes via automated high-frequency sampling – David M Needham – bioRxiv

Food microbiology

Pre-print: Fusicatenibacter Is Associated with Kefir Drinking – Richard Sprague – bioRxiv


A novel double-layer mucoadhesive tablet containing probiotic strain for vaginal administration: Design, development and technological evaluation – María Teresa Sánchez – European Journal of Pharmaceutical Sciences

Efficacy and Safety of a Multistrain Probiotic Formulation Depends from Manufacturing – Vito Trinchieri – Frontiers in Immunology

Phages and viruses

Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana – Arielle Salmier – PLOS ONE

Review: The enigmatic archaeal virosphere – David Prangishvili – Nature Reviews Microbiology


Old meets new: most probable number validation of metagenomic and metatranscriptomic datasets in soil – Tim H Mauchline – Letters in Applied Microbiology

Pre-print: AQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome – Xiao-Tao Jiang – bioRxiv


Review: Mass spectrometry-based metabolomics: Targeting the crosstalk between gut microbiota and brain in neurodegenerative disorders – Hemi Luan – Mass Spectrometry Reviews

Pre-print: Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function – Chase Clark – bioRxiv


Evaluating in vitro culture medium of gut microbiome with orthogonal experimental design and metaproteomics approach – Leyuan Li – Journal of Proteome Research

More microbes

Pre-print: Chemotaxis allows bacteria to overcome host-generated reactive oxygen species that constrain gland colonization – Kieran D Collins – bioRxiv

Microbes in the news

Specimens of Earth’s Oldest Known Life Forms Have Been Discovered in Tasmania – Michelle Starr – Science Alert

Shape-shifting agent targets harmful bacteria in the stomach – Phys.Org

Opinion: Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance? – Lito E Papanicolas – Trends in Microbiology

Microbes on the market

A Silicon Valley Startup Wants Women To Test Their Vaginal Microbiota At Home – Ellie Kincaid – Forbes

Seres teams with cancer heavyweights for microbiome-checkpoint inhibitor combination trial – Nick Paul Taylor – FierceBiotech

November 14, 2017

Today seems unusually quiet. But, a few highlights still stand out. Scientists discover a new mechanism of antibiotic resistance. The HHS in the US released a progress report on fighting against antibiotic resistance. Finally, please enjoy the stunning beauty of microbes under the microscope.


Grants Alert – Federal Grants & Contracts


Technologist (Microbiology) – Tampa Florida

General microbiology

New issue of Global Change Biology Bioenergy

* The multiple antibiotic resistance operon of enteric bacteria controls DNA repair and outer membrane integrity – Prateek Sharma et al. – Nature Communications

Press: New mechanisms discovered that bacteria use to protect themselves from antibiotics –

* National Action Plan Drives Progress in Fight Against Antibiotic-Resistant Bacteria – Christopher M. Jones – HHS

Na+-induced structural transition of MotPS for stator assembly of the Bacillus flagellar motor – Naoya Terahara et al. – Science Advances

Press: How bacteria get their groove: Mechanism behind flagellar motility – Osaka University – Science Daily

Phages and viruses

Phage Genome Annotation Using the RAST Pipeline – Katelyn McNair et al. – Bacteriophages

Microbes in the news

* Seeing the Beautiful Intelligence of Microbes – John Rennie & Lucy Reading-Ikkanda – Quanta Magazine

FDA Acts to Advance Potential Inhaled Treatment of Resistant Bacteria Tied to Lung Infections – Janet Stewart – Cystic Fibrosis News Today

Strong Evidence Emerging That Gut Microbiome Is a Key Variable in Immunotherapy Efficacy – Theodore Bosworth – Medscape

How the Gut Microbiome Affects Outcomes in HIV – Jeannette Y. Wick – Special Pharmacy Times

Microbes on the market

With a grain of salt: Would you put bacteria on your face? This brand thinks you should – Victoria Hall – Telegraph


November 13, 2017

Today’s digest is concise but exciting- how electric bandages decrease biofilm formation and highlights on immune response and microbiome interactions

General microbiome

Differences in bacterial composition between men’s and women’s restrooms and other common areas within a public building. Dobbler PCT. Antonie van Leeuwenhoek

Gut microbiome 

The Intestinal Microbiome in Nonalcoholic Fatty Liver Disease.Puri P. Clinics in Liver Disease

Lung microbiome

Highlights in immune response, microbiome and precision medicine in allergic disease and asthma. Sokolowska M. Current Opinion in Immunology

Animal microbiome

Evidence from the gut microbiota of swarming alates of a vertical transmission of the bacterial symbionts in Nasutitermes arborum (Termitidae, Nasutitermitinae). Diouf M- Antonie van Leeuwenhoek

Captive bottlenose dolphins and killer whales harbor a species-specific skin microbiota that varies among individuals. Chiarello M,

Microbiome News

Electric bandages help to fight infection– Digital Journal