May 22, 2017

Events and jobs
Microscopist Asbestos/Microbiology – EMSL Analytical, Seattle, WA

Technician (Microbiology Team) – AsureQuality (AQ), Christchurch, Canterbury, New Zealand

Laboratory Technician I (Microbiology & Genetics) – IDEXX, Columbia, MO, US

Associate Scientist Molecular Microbiology – CheckMark Labrecruitment, South Holland

Human respiratory microbiome
Review: Infection-mediated asthma: etiology, mechanisms and treatment options, with focus on Chlamydia pneumoniae and macrolides – Wilmore C. Webley – Respiratory Research

Human gut microbiome
Review: The bidirectional gut-brain-microbiota axis as a potential nexus between traumatic brain injury, inflammation, and disease – Mark Sundman – Brain, Behavior, and Immunity

Clinical Trial Watch: ‘Targeting the gut-liver axis in liver disease’ – Reiner Wiest – Journal of Hepatology

Gluten-degrading bacteria are present in the human small intestine of healthy volunteers and celiac patients – Alexandra R. Herran – Research in Microbiology

The sialate O-acetylesterase EstA from gut Bacteroidetes species enables sialidase-mediated cross-species foraging of 9-O-acetylated sialoglycans – Lloyd S. Robinson – Journal of Biological Chemistry

Plant, root, and soil microbiome
Seasonal soil microbial responses are limited to changes in functionality at two Alpine forest sites differing in altitude and vegetation – José A. Siles A. Siles – Scientific Reports

Review: Evolutionary Ecology of Multitrophic Interactions between Plants, Insect Herbivores and Entomopathogens – Ikkei Shikano – Journal of Chemical Ecology

Pseudomonas chlororaphis produces two distinct R-tailocins that contribute to bacterial competition in biofilms and on roots – Robert J. Dorosky – Applied and Environmental Microbiology

Water and extremophile microbiome
Review: A multiomics approach to study the microbiome response to phytoplankton blooms – Liyan Song – Applied Microbiology and Biotechnology

Antibiotics/probiotics/prebiotics
The Resistome Of Important Human Pathogens – Christian Munck – bioRxiv

Phages and viruses
Embracing the enemy: the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer – Marie Touchon – Current Opinion in Microbiology
Part of a themed issue on MGE-HGT in prokaryotes

Bioinformatics
StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees – Märt Roosaare – PeerJ

Microbes in the news
Bacteria could lead to cleaner methane power – Jon Fingas – Engadget

Luminous bacteria will help to measure radioactivity – Siberian Federal University – EurekAlert!

A ‘Superbug’ Fungus Is Spreading Across The US – Kristen V. Brown – Gizmodo

Research shows that gut bacteria tells their hosts what to eat – Cordis News

Indian researchers use a novel route to kill TB bacteria – R. Prasad – The Hindu

Bacteria Hysteria
Cash is even grosser than you knew: Dangerous bacteria survive on paper money, study finds – James Dennin – AOL

May 8, 2017

First, a job opportunity in my PI’s lab: please forward or apply! Papers today are spread over multiple topics, with more in soil and water, and an emphasis on ecological ideas for the general microbiome.

Events and jobs
Bioinformatics Research Associate – Harvard T.H. Chan School of Public Health

General microbiome
Perspective: Multi-stability and the origin of microbial community types – Didier Gonze – ISME

Microbial consortia at steady supply – Thibaud Taillefumier – eLife

Human oral microbiome
Natural Competence Is Common among Clinical Isolates of Veillonella parvula and Is Useful for Genetic Manipulation of This Key Member of the Oral Microbiome – Steven Knapp – Frontiers in Cellular and Infection Microbiology

Human gut microbiome
Opinion: What happened to Koch’s Postulates in Diarrhea? – Shamima Sultana – Environmental Microbiology

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics – Sonny T.M. Lee – Microbiome

Animal experiments
TCDD influences reservoir of antibiotic resistance genes in murine gut microbiome – Robert D. Stedtfeld – FEMS Microbiology Ecology

A Metagenomics Investigation of Carbohydrate-Active Enzymes along the Gastrointestinal Tract of Saudi Sheep – Saad Al-Masaudi – Frontiers in Microbiology

Plant, root, and soil microbiome
Vertical distribution of microbial communities in soils contaminated by chromium and perfluoroalkyl substances – Bingxin Li – Science of the Total Environment

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations – Yunfu Gu – PLoS One

Soil microbial community composition in tallgrass prairie restorations converge with remnants across a 27-year chronosequence – Nicholas A. Barber – Environmental Microbiology

Arbuscular and Ectomycorrhizal Fungi Associated with the Invasive Brazilian Pepper Tree (Schinus terebinthifolius) and Two Native Plants in South Florida – Karim Dawkins – Frontiers in Microbiology

Water and extremophile microbiome
Differential responses of marine, mesohaline, and oligohaline bacterial communities to the addition of terrigenous carbon – DPR Herlemann – Environmental Microbiology

Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia – Hauke F. Kegler – Frontiers in Microbiology

Built environment
Long-term successional dynamics of microbial association networks in anaerobic digestion processes – Linwei Wu – Water Research

Non-denitrifying polyphosphate accumulating organisms obviate requirement for anaerobic condition – A. Anisa Cokro – Water Research

Probiotics / prebiotics
Review: Effectiveness of Probiotic, Prebiotic, and Synbiotic Therapies in Reducing Postoperative Complications: A Systematic Review and Network Meta-analysis – Nongyao Kasatpibal – Clinical Infectious Diseases

Review: Effect of Probiotics on Metabolic Outcomes in Pregnant Women with Gestational Diabetes: A Systematic Review and Meta-Analysis of Randomized Controlled Trials – Bonnie L. Taylor – Nutrients

Techniques
Rapid Pathogen Identification in Bacterial Pneumonia Using Real-time Metagenomics – Kathryn M Pendleton – American Journal of Respiratory and Critical Care Medicine

The Type of Forage Substrate Preparation Included as Substrate in a RUSITEC System Affects the Ruminal Microbiota and Fermentation Characteristics – Andrea C. Duarte – Frontiers in Microbiology

Microbes in the news
Gold processing bacteria help to recycle electronics – Tim Sandle – Digital Journal

Continued exposure to bacteria from decomposing bodies took its toll on workers – Mahesh Avadhuta – Deccan Chronicle

Bacteria Hysteria
Rob Mancini: Why do folks insist on providing bad food safety advice? – Ben Chapman – BarfBlog

April 17, 2017

A light digest for Marathon Monday. For me, the highlights today are under “Microbes in the News”, with amazing papers on viral/bacterial detection, bacterial cell size, and cluster regulation!

Human nearly-sterile sites
Evidence for polymicrobial communities in explanted vascular filters and atheroma debris – Jeremy E. Ellis – Molecular and Cellular Probes

Plant, root, and soil microbiome
Global-scale structure of the eelgrass microbiome – Ashkaan K. Fahimipour – Applied Environmental Microbiology
Note: Published as a pre-print back on November 28, 2016

Built environment
Comparing the impact of ultrafine particles from petrodiesel and biodiesel combustion to bacterial metabolism by targeted HPLC-MS/MS metabolic profiling – Fanyi Zhong – Ecotoxicology and Environmental Safety

Revealing the bacterial profile of an anoxic-aerobic moving-bed biofilm reactor system treating a chemical industry wastewater – Joao P Bassin – International Biodeterioration & Biodegradation

Probiotics / prebiotics
An extracellular cell-attached pullulanase confers branched α-glucan utilization in human gut Lactobacillus acidophilus – Marie S Moller – Applied and Environmental Microbiology

Phages and viruses (and transfers)
Class 1 integrons as invasive species – Michael R Gillings – Current Opinion in Microbiology

Bioinformatics
MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers – Cedric Chauve – bioRxiv

Techniques
Validation and application of an ultrahigh-performance liquid chromatographic-Orbitrap mass spectrometric method for the simultaneous detection and quantification of volatile and non-volatile organic acids in human faecal samples – Claudio Gardana – Journal of Pharmaceutical and Biomedical Analysis

Impact of wet aerobic pretreatments on cellulose accessibility and bacterial communities in rape straw – Jiang-Hao Tian – Bioresource Technology

Nanopore detection of bacterial DNA base modifications – Alexa B.R. McIntyre – bioRxiv

Microbes in the news
Novel CRISPR Tool Rapidly Detects Viruses And Bacteria – Milla Bengtsson – ReliaWire
Original paper: Nucleic acid detection with CRISPR-Cas13a/C2c2 – Jonathan S. Gootenberg – Science

Study discovers fundamental unit of cell size in bacteria – UCSD – EurekAlert
Invariance of Initiation Mass and Predictability of Cell Size in Escherichia coli – Fangwei Si – Current Biology

Mini-Factories For Drugs? Researchers Find A Way To Switch On ‘Silent’ Gene Clusters In Bacteria – Avaneesh Pandey – International Business Times
Original paper: Discovery of scmR as a global regulator of secondary metabolism and virulence in Burkholderia thailandensis E264 – Dainan Mao – PNAS

April 3, 2017

Pregnancy and early life
Nasopharyngeal microbiome in premature infants and stability during rhinovirus infection – Geovanny F Perez – Journal of Investigative Medicine

Human respiratory microbiome
Abstract: (109) – The Microbiome of the Respiratory Tract After Heart Transplantation – H. Joyce – The Journal of Heart and Lung Transplantation

Human vaginal microbiome
Trichomonas vaginalis infection in symbiosis with Trichomonasvirus and Mycoplasma – Raina Fichorova – Research in Microbiology

Higher prevalence of colonization with Gardnerella vaginalis and gram-negative anaerobes in patients with recurrent miscarriage and elevated peripheral natural killer cells – R.J. Kuon – Journal of Reproductive Immunology

Human gut microbiome
Review: Gut microbiota and renal transplant outcome – Mohammadreza Ardalan – Biomedicine & Pharmacotherapy

Review: Non-alcoholic fatty liver disease: An update with special focus on the role of gut microbiota – Michael Doulberis – Metabolism

Prebiotic efficacy and mechanism of inulin combined with inulin-degrading Lactobacillus paracasei I321 in competition with Salmonella – Pochanart Kanjan – Carbohydrate Polymers

Animal experiments
Conditional Postnatal Deletion of the Neonatal Murine Hepatic Circadian Gene, Npas2, Alters the Gut Microbiome Following Restricted Feeding – Derek S. O’Neil – American Journal of Obstetrics and Gynecology

Bacterial Signatures of “Red-Operculum” Disease in the Gut of Crucian Carp (Carassius auratus) – Tongtong Li – Microbial Ecology

Microbiota analysis of environmental slurry and its potential role as a reservoir of bovine digital dermatitis pathogens – Kirstine Klitgaard – Applied and Environmental Microbiology

Black-pigmented anaerobic bacteria associated with ovine periodontitis – Ana C. Borsanelli – Veterinary Microbiology

Plant, root, and soil microbiome
The tale of a neglected energy source: Elevated hydrogen exposure affects both microbial diversity and function in soil – Mondher Khdhiri – Applied and Environmental Microbiology

Fungal community in olive fruits of cultivars with different susceptibilities to anthracnose and selection of isolates to be used as biocontrol agents – Gilda Preto – Biological Control

Water and extremophile microbiome
Microbial profiles of a drinking water resource based on different 16S rRNA V regions during a heavy cyanobacterial bloom in Lake Taihu, China – Junyi Zhang – Environmental Science and Pollution Research

Pathogenic potentials of Aeromonas species isolated from aquaculture and abattoir environments – Isoken H. Igbinosa – Microbial Pathogenesis

Built environment
Different methods used to form oxygen reducing biocathodes lead to different biomass quantities, bacterial communities, and electrochemical kinetics – Mickael Rimboud – Bioelectrochemistry

Food microbiology
Characterization of bacterial communities of donkey milk by high-throughput sequencing – Maria de los Dolores Soto del Rio – International Journal of Food Microbiology

Prebiotic effect of xylooligosaccharides produced from birchwood xylan by a novel fungal GH11 xylanase – Manuel Nieto-Dominguez – Food Chemistry

Adsorption of aflatoxin B1, zearalenone and ochratoxin A by microorganisms isolated from Kefir grains – Fadia Ben Taheur – International Journal of Food Microbiology

Identification and characterization of lactic acid bacteria and yeasts of PDO Tuscan bread sourdough by culture dependent and independent methods – Michela Palla – International Journal of Food Microbiology

Review: African fermented dairy products – Overview of predominant technologically important microorganisms focusing on African Streptococcus infantarius variants and potential future applications for enhanced food safety and security – Christoph Jans – International Journal of Food Microbiology

Probiotics / prebiotics
Review: Strategies to promote abundance of Akkermansia muciniphila, an emerging probiotics in the gut, evidence from dietary intervention studies – Kequan Zhou – Journal of Functional Foods

A randomized trial to determine the impact of a digestion resistant starch composition on the gut microbiome in older and mid-age adults – Michelle J. Alfa – Clinical Nutrition

Effects of synbiotics on immunity and disease resistance of narrow-clawed crayfish, Astacus leptodactylus leptodactylus (Eschscholtz, 1823) – Omid Safari – Fish & Shellfish Immunology

Review: The role of microbiota in allergy development – Monika Marko – Alergologia Polska (Polish Journal of Allergology)

Phages and viruses
Synergistic elimination of bacteria by phage and the innate immune system – Chung Yin – bioRxiv

Techniques
Simulated Ribosomal RNA:DNA Ratios Show Potential to Misclassify Active Populations as Dormant – Blaire Steven – Applied and Environmental Microbiology

Microbes in the news
Gut microbiota hold keys to childhood undernutrition – Healio

Would You Drink a Probiotic with the Gut Bacteria of Elite Athletes? – Terrence McNally – Huffington Post

You’re probably showering way too often – Rafi Letzter – Business Insider

How often should you clean your toilet, your bed sheets, the fridge and your make-up bag? – Zoe Cripps – Mirror

Microbes on the market
Seres Therapeutics Inc (MCRB) Short Interest Update – Daniel Jordon – Sports Perspectives and Market News

Bacteria Hysteria
A healthier flatter tummy in just SIX weeks: The secrets of feeling great – and losing weight – by keeping your ‘friendly bacteria’ happy – Liz Earle – DailyMail

March 20, 2017

There were almost no papers this weekend, so today’s digest is short.

Events and jobs

Assistant Professor of Horticulture – Plant Microbiome Research – University of Kentucky

Postdoctoral Scientist – Microbiome, Mycobiome, Mucosal Immunology – Weill Cornell Medicine, New York City

Water and extremophile microbiome

Whole community metagenomics in two different anammox configurations: process performance and community structure – Ananda S. Bhattacharjee – Environmental Science Technology

Phages and viruses

All of today’s posts are genome announcements:
Genomic Characterization of Three Melon Necrotic Spot Viruses Detected in Human Stool Specimens – Rachel Marine – Genome Announcements

Genome Sequence of Cauliflower Mosaic Virus Identified in Earwigs (Doru luteipes) through a Metagenomic Approach – Márcio Tadeu Godinho – Genome Announcements

Bioinformatics

metaSPAdes: a new versatile metagenomic assembler – Sergey Nurk – Genome Research

Science, publishing, and career

All biology is computational biology – Florian Markowetz – PLoS Biology

No – all biology is not computational biology – Jonathan Eisen – Tree of Life

March 2, 2017

Events and jobs
Postdoctoral Teaching and Learning Fellow in Microbiome Data Analysis – Department of Microbiology and Immunology (MICB) – University of British Columbia

Commercial Support Manager, Probiotics for Human Health & Microbiome – Hørsholm, Denmark – Chr. Hansen

Position in experimental biochemistry including microbiology – University of Warsaw

Microbiology Laboratory Technician – Milwaukee, WI – Aerotek

Human vaginal microbiome
Specific vaginal lactobacilli suppress the inflammation induced by lipopolysaccharide stimulation through downregulation of toll-like receptor 4 expression in human embryonic intestinal epithelial cells – Keisuke Tobita – Bioscience of Microbiota, Food and Health

Human gut microbiome
Editorial: The gut microbiota and psychiatric illness – Glenda MacQueen – Journal of Psychiatry and Neurosciece

Animal experiments
Understanding the mechanisms of zinc bacitracin and avilamycin on animal production: linking gut microbiota and growth performance in chickens – Eduardo Crisol-Martínez – Applied Microbiology and Biotechnology

Transition of the intestinal microbiota of dogs with age – Hiroaki Masuoka – Bioscience of Microbiota, Food and Health

Faecal microbiota transplantation protects against radiation-induced toxicity – Ming Cui – EMBO Molecular Medicine

Animal microbiome
Comparative analysis of gut microbiota of mosquito communities in central Illinois – Ephantus J. Muturi – PLoS Neglected Tropical Diseases

Plant, root, and soil microbiome
Community Structure, Species Variation, and Potential Functions of Rhizosphere-Associated Bacteria of Different Winter Wheat (Triticum aestivum) Cultivars – Aaron K Mahoney – Frontiers in Plant Science

Water and extremophile microbiome
Microbial community assembly and evolution in subseafloor sediment – Piotr Starnawski – PNAS

Phylogenetic Diversity and Anti-MRSA Activity of Halotolerant Actinobacteria from sediments in Great Salt Plains, Oklahoma – Ahmed H Gad – bioRxiv

Investigating the Microbial Degradation Potential in Oil Sands Fluid Fine Tailings Using Gamma Irradiation: A Metagenomic Perspective – Danielle VanMensel – Microbial Ecology

Food microbiology
Boswellia serrata resin extract alleviates azoxymethane (AOM)/dextran sodium sulfate (DSS)-induced colon tumorigenesis – YC Chou – Molecular Nutrition Food Research

A series of review articles on the FODMAP diet has been published in the most recent issue of the Journal of Gastroenterology and Hepatology
Review: Use of the low-FODMAP diet in inflammatory bowel disease – Peter R Gibson – Journal of Gastroenterology and Hepatology
Review: How to institute the low-FODMAP diet – Jacqueline S Barrett – Journal of Gastroenterology and Hepatology
Review: When the low FODMAP diet does not work – Emma P Halmos – Journal of Gastroenterology and Hepatology
Review: Nutritional, microbiological and psychosocial implications of the low FODMAP diet – Heidi Maria Staudacher – Journal of Gastroenterology and Hepatology

The spxB gene as a target to identify Lactobacillus casei group species in cheese – Maria Luisa Savo Sardaro – Food Microbiology

Bioinformatics
GMPR: A novel normalization method for microbiome sequencing data – Jun Chen – bioRxiv

Cohesion: A method for quantifying the connectivity of microbial communities – Cristina Herren – bioRxiv

Techniques
Microbial population dynamics in continuous anaerobic digester systems during start up, stable conditions and recovery after starvation – Nadieh de Jonge – Bioresource Technology

Microbes in the news
How Bacteria Interfere with Insect Reproduction – Ruth Williams – The Scientist
This references two important papers on Wolbachia:
A Wolbachia deubiquitylating enzyme induces cytoplasmic incompatibility – John F Beckmann – Nature Microbiology
Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility – Daniel P LePage – Nature

Synopsis: Racing Bacteria – Katherine Wright – APS Physics

Meet green bacteria, airport’s eco-friendly toilet cleaners – Times of India

Assessing Host-Microbiota Relationships – Richard A Stein – Genetic Engineering and Biotechnology News

Bacteria from the ancient city of Troy – Caitlin Pepperell – Microbe Post

Gut bacteria determines the beneficial impacts of soy food on heart health – David Templeton – Pittsburgh Post-Gazette

Microbes on the market
Vaginal Microbiota May Affect Tenofovir Applied Intravaginally – John Schieszer – Infectious Disease Advisor

The Human Microbiome: Advancing New Frontiers in a Rapidly Emerging Market – PR Newswire – Yahoo Finance

New research data published in Frontiers in Microbiology confirm the microbiome’s potential to impact plant health – PR Newswire – Yahoo Finance

Microbiome Therapeutics Market Growth, Forecast and Value Chain 2017-2027 – Future Market Insights – OpenPR

Random Science
Editorial: Microbiome yarns: microbiomology of curly and straight hair – Kenneth Timmis – Microbial Biotechnology

February 21, 2017

Events and jobs
Microbiology Analyst Level II – DTS Food Laboratories – Brisbane, AU

Microbial Menagerie is profiling #ActualLivingScientists, especially microbiologists! Visit here for more information, or sign up here!

4th International Symposium on the Environmental Dimension of Antibiotic Resistance – Aug 13-17, 2017 in Lansing, MI

5th Molecular Microbiology Meeting & 4th Midlands Molecular Microbiology Meeting (M4) – Sept 13-14, 2017 in Birmingham, UK

General microbiome
Metagenomic DNA sequencing for the diagnosis of intraocular infections – Thuy Doan – bioRxiv

Human skin microbiome
Bacterial biofilm in chronic lesions of hidradenitis suppurativa – H.C. Ring – British Journal of Dermatology

Human gut microbiome
Review: Bile acid control of metabolism and inflammation in obesity, type 2 diabetes, dyslipidemia and NAFLD – Oscar Chavez-Talavera – Gastroenterology

Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients – Eli Moss – bioRxiv

Isolation and high-dimensional phenotyping of gastrointestinal immune cells – Bruna A. David – Imumunology
Not focused on microbes – but may be of use to those working with these cells!

Water and extremophile microbiome
Oxygenic and anoxygenic photosynthesis in a microbial mat from an anoxic and sulfidic spring – Dirk de Beer – Environmental Microbiology

A six thousand-year record of climate and land-use change from Mediterranean seagrass mats – Lourdes Lopez-Merino – Journal of Ecology
There is a hidden section on fungi.

High-Throughput Metabolic Network Analysis and Metatranscriptomics of a Cosmopolitan and Streamlined Freshwater Lineage – Joshua J Hamilton – bioRxiv

Are oceanic fronts ecotones? Seasonal changes along the Subtropical Front show fronts as bacterioplankton transition zones but not diversity hotspots – Sergio E Morales – bioRxiv

Built environment
Genome-resolved metagenomics of a bioremediation system for degradation of thiocyanate in mine water containing suspended solid tailings – Sumayah F. Rahman – MicrobiologyOpen

Comparative analysis of metagenomes of Italian top soil improvers – F. Gigiliucci – Environmental Research
This does not seem available yet, so PubMed is linked rather than the paper.

Food microbiology
Diversity analysis and quantification of lactic acid bacteria in traditionally fermented yaks’ milk products from Tibet – Yan Ren – Food Biotechnology

Phages and viruses
Review: Risk of waterborne virus spread – review of survival of relevant fish and crustacean viruses in the aquatic environment and implications for control measures – Birgit Oidtmann – Reviews in Aquaculture

Microbial interactions
Local interactions lead to spatially correlated gene expression levels in bacterial groups – Simon van Vliet – bioRxiv

Science, publishing, and career
Broad Institute prevails in heated dispute over CRISPR patents – Sharon Begley – STAT News, along with six takeaways.