Category Archives: Water microbiome

June 28, 2016

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A fundraiser to study the turtle microbiome, multiple sclerosis, generalists inside specialist, and visualizing translational activity.

Events

IndieGoGo campaign: TurtleTracts: Study Microbes to Save Sea Turtles – Aubrey Tauer

Also see this blog post: Sneak Peak at our Sea Turtle Microbiome Initiative – Aubrey Tauer

Pregnancy and birth

Gut bacteria and late-onset neonatal bloodstream infections in preterm infants – Phillip I. Tarr – Seminars in Fetal and Neonatal Medicine

Human respiratory microbiome

Commentary: Mode of delivery to the brave new (microbial) world: a defining moment for the respiratory microbiome? – Georgios D. Kitsios – EBioMedicine

Human gut microbiome

Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls – Jun Chen – Scientific Reports

Press: Link between gut bacteria, MS discovered. MS patients show lower levels of good bacteria – Science Daily

Review: Microbiota as Therapeutic Targets – Xavier R.J. – Digestive Diseases

Animal microbiome
The Generalist Inside the Specialist: Gut Bacterial Communities of Two Insect Species Feeding on Toxic Plants Are Dominated by Enterococcus sp. – Cristina Vilanova – Frontiers in Microbiology

Review: The gut microbiome as a virtual endocrine organ with implications for farm and domestic animal endocrinology – T.F. O’Callaghan – Domestic Animal Endocrinology

Plant, root, and soil microbiome
Systemic enrichment of antifungal traits in the rhizosphere microbiome after pathogen attack – Jan-Hendrik Dudenhöffer – Journal of Ecology

A multi-biological assay approach to assess microbial diversity in arsenic (As) contaminated soils – S.R. Stazi – Geomicrobiology Journal

Effects of two fungicide formulations on microbial and macroinvertebrate leaf decomposition under laboratory conditions – Adria A. Elskus – Environmental Toxicology and Chemistry

Book: Plant, Soil and Microbes – Editors: Khalid Rehman Hakeem, Mohd Sayeed Akhtar – Springer

Water and extremophile microbiome

Metagenomics-Guided Mining of Commercially Useful Biocatalysts from Marine Microorganisms – A.R. Uria – Advances in Food and Nutrition Research

Lessons learned from thirty years of geomicrobiological studies of Río Tinto – Ricardo Amils – Research in Microbiology

Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments – Xian Zhang – Environmental Microbiology Reports

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill – Nina Dombrowski – Nature Microbiology

News and views: Marine microbiology: Community clean up – Rachel Mackelprang – Nature Microbiology

Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses – M. Tangherlini – Scientific Reports

Marine phage genomics: the tip of the iceberg – Blanca Perez Sepulveda – Microbiology Letters

Metabolic networks and proteomics

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota – Xu Zhang – Microbiome

The use of propidium monoazide in conjunction with qPCR and Illumina sequencing to identify and quantify live yeasts and bacteria – Mansak Tantikachornkiata – International Journal of Food Microbiology

Protocol: Constructing and Analyzing Metabolic Flux Models of Microbial Communities – José P. Faria – Springer Protocols

Viruses and phages

Opinion: The Janus-Face of Bacteriophages across Human Body Habitats – Adam Wahida – PLOS Pathogens

Review: Research on the human virome: where are we and what is next – Shimian Zou – Microbiome

Microbial ecology and techniques

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia – Roland Hatzenpichler – PNAS

Press: See and sort: Developing novel techniques to visualize uncultured microbial cell activity – Science Daily

High functional diversity stimulates diversification in experimental microbial communities – Alexandre Jousset – Science Advances

Measuring the biodiversity of microbial communities by flow cytometry – Ruben Props – Methods in Ecology and Evolution

Highlight: A timely reminder of technical limitations – James I. Prosser – Microbial Biotechnology

Species-sorting and mass-transfer paradigms control managed natural metacommunities – Susanne Günther – Environmental Microbiology

Microbes in the news

Slimy clumps of bacteria kill thousands. Scientists are fighting back – Usha Lee McFarling – STAT News

Why everyone’s suddenly talking about gut bacteria – Laura Entis – Fortune

Scientists find link between makeup of individual’s microbiome and head and neck cancer – News Medical

June 26, 2016

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Pregnancy and birth

A key genetic factor for fucosyllactose utilization affects infant gut microbiota development – Takahiro Matsuki – Nature Communications

Necrotizing enterocolitis and preterm infant gut bacteria – Barbara B. Warner – Seminars in Fetal & Neonatal

Human oral microbiome

Identification of Veillonella Species in the Tongue Biofilm by Using a Novel One-Step Polymerase Chain Reaction Method – Izumi Mashima – PLOS ONE

Human respiratory microbiome

Bacterial Microbiota Analysis Present in the Nose and Pharynx of a Mexican Young Population – Ana Karina Rodríguez-Vicente – Int J Curr Microbiol App Sci

Human gut microbiome

Significant Differences Found in Short Nucleotide Sequences of Human Intestinal Metagenomes of Northern-European and Chinese Origin – Balázs Szalkai – Biochimica et Biophysica Acta (BBA) – General Subjects

Analysis of the effects of microbiome-related confounding factors on the reproducibility of the volatolomic test – Marcis Leja – Journal of Breath Research

Campylobacter concisus utilizes blood but not short chain fatty acids despite showing associations with Firmicutes taxa – Nadeem O. Kaakoush – Microbiology

Review: Links Between the Microbiome and Bone – C.J. Hernandez – Journal of Bone and Mineral Research

Review: Microbiome, Metabolome and Inflammatory Bowel Disease – Ishfaq Ahmed – Microorganisms

Comment: Ethics of exploring the microbiome of native peoples – Maria G. Dominguez-Bello – Nature Microbiology

Microbes found in blood

I’m skeptical about this review: A Bacterial Component to Alzheimer’s-Type Dementia Seen via a Systems Biology Approach that Links Iron Dysregulation and Inflammagen Shedding to Disease – Etheresia Pretorius – Journal of Alzheimer’s Disease

Animal experiments

A sentinel goblet cell guards the colonic crypt by triggering Nlrp6-dependent Muc2 secretion – George M. H. Birchenough – Science

Gut microbiota drive the development of neuro-inflammatory response in cirrhosis – Dae Joong Kang – Hepatology

Bacteriophage infections of microbiota can lead to leaky gut in an experimental rodent model – George Tetz – Gut Pathogens

The Effects of LW-AFC on Intestinal Microbiome in Senescence-Accelerated Mouse Prone 8 Strain, a Mouse Model of Alzheimer’s Disease – Jianhui Wang – Journal of Alzheimer’s Disease

Microbiome associations in pigs with the best and worst clinical outcomes following co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) – Megan C. Niederwerder – Veterinary Microbiology

Press: College of Veterinary Medicine researchers examine microbiome associations related to disease expression in swine – Kansas State University

Supplementing Blends of Sugars, Amino Acids, and Secondary Metabolites to the Diet of Termites (Reticulitermes flavipes) Drive Distinct Gut Bacterial Communities – Xing-Feng Huang – Microbial Ecology

Letter: Does Intestinal Microbiota Protect Mice Against Acute/Binge Drinking-Induced Liver Injury? – Tao Zeng – Alcoholism: Clinical and Experimental Research

Animal microbiome

DGGE: Influence of Starvation on the Structure of Gut-Associated Bacterial Communities in the Chinese White Pine Beetle (Dendroctonus armandi) – Xia Hu – Forests

Plant, root, and soil microbiome

Effects of temperature variability on community structure in a natural microbial food web – Axel Zander – Global Change Biology

Effectiveness of ecological rescue for altered soil microbial communities and functions – Kadiya Calderón – ISME Journal

Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition – Carles Castaño – Mycorrhiza

Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters – Weichen Bao – Scientific Reports

Water and extremophile microbiome

Revealing the relationship between microbial community structure in natural biofilms and the pollution level in urban rivers: a case study in the Qinhuai River Basin, Yangtze River Delta – Wei Cai – Water Science and Technology

Status of metal pollution in rivers flowing through urban settlements at Pune and its effect on resident microflora – Neelu Nawani – Biologia

Profiling of Sediment Microbial Community in Dongting Lake before and after Impoundment of the Three Gorges Dam – Wei Huang – Int. J. Environ. Res. Public Health

Bioreactor and wastewater microbiology

Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water – Junying Tang – Ecotoxicology and Environmental Safety

Food microbiology

Effect of Simulated Sanitizer Carryover on Recovery of Salmonella from Broiler Carcass Rinsates – Gary R. Gamble – Journal of Food Protection

Press: USDA Salmonella Bacteria on Chicken Testing Severely Flawed, New Study Finds – Emily Monaco – Organic Authority

Potential applications of metagenomics to assess the biological effects of food structure and function – Tasha Santiago-Rodriguez – Food & Function

Bioinformatics and metagenomics

A comparison of tools for the simulation of genomic next-generation sequencing data – Merly Escalona – Nature Reviews Genetics

Hessian Regularization Based Symmetric Nonnegative Matrix Factorization for Clustering Gene Expression and Microbiome Data – Yuanyuan Ma – Methods

Techniques

Grown, Printed, and Biologically Augmented: An Additively Manufactured Microfluidic Wearable, Functionally Templated for Synthetic Microbes – Christoph Bader – 3D Printing and Additive Manufacturing

Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning – Lucia Kraková – Extremophiles

DGGE: Representative sampling of natural biofilms: influence of substratum type on the bacterial and fungal communities structure – Jennifer Hellal – Springer Plus

More microbiology

Applying landscape genetics to the microbial world – Rachael Y. Dudaniec – Molecular Ecology

A metapopulation model for the spread of MRSA in correctional facilities – Marc Beauparlant – Infectious Disease Modelling

Biological Dual-Use Research and Synthetic Biology of Yeast – Angela Cirigliano – Science and Engineering Ethics

Microbes in the news

Fabulous Pacific coast and the latest digestive diseases research: BMC Medicine joins DDW2016 – Alessandro Recchioni – BioMedCentral blog

The Unseen – Millions of microbes are yet to be discovered. Will one hold the ultimate cure? – Raffi Khatchadourian – The New Yorker

Indicator of chronic fatigue syndrome found in gut bacteria – Krishna Ramanujan – Cornell Chronicle

Fermentation Fervor: Here’s How Chefs Boost Flavor And Health – Allison Aubrey – NPR Morning Edition

Beneficial bacteria may protect breasts from cancer – ASM – EurekAlert

Economics in Mind, Evolution Has Allowed Some Bacteria to Evolve Sublime Genomes – Aswin Sai Narain Seshasayee – The Wire

Old Technology Successfully Reduce Salmonella in Meat Products by 90 Percent –  John Raphael – Nature World News

Bright Minds Battling Dark Diseases: San Diego is home to world-class biomedical scientists focused on cutting-edge projects touted by president – Gary Robbins – The San Diego Union Tribune

Liquid eyeliner recalled, contains bacteria – CTV News Winnipeg

June 24, 2016

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Placenta samples not distinguishable from controls, gut microbiome in ME/CFS and PKU patients, childhood undernutrition, corals’ microbial sentinels, and plant root traps.

Pregnancy and birth

I was hoping for this study to be done: Comparison of placenta samples with contamination controls does not provide evidence for a distinct placenta microbiota – Abigail P. Lauder – Microbiome

Systematic review: Treatment of bacterial vaginosis in pregnancy in order to reduce the risk of spontaneous preterm delivery – a clinical recommendation – Thor Haahr – Acta Obstetricia et Gynecologica Scandinavica

Human ear microbiome

The microbiome of otitis media with effusion – Chun Ling Chan – The Laryngoscope

Human gut microbiome

Reduced diversity and altered composition of the gut microbiome in individuals with myalgic encephalomyelitis/chronic fatigue syndrome – Ludovic Giloteaux – Microbiome

Phenylketonuria and Gut Microbiota: A Controlled Study Based on Next-Generation Sequencing – Felipe Pinheiro de Oliveira – PLOS ONE

Review: Childhood undernutrition, the gut microbiota, and microbiota-directed therapeutics – Laura V. Blanton – Science

Editorial: Gut microbiota and undernutrition – Caroline Ash – Science

Infection and microbiology

Role of Clinicogenomics in Infectious Disease Diagnostics and Public Health Microbiology – Lars F. Westblade – Journal of Clinical Microbiology

Novel Taxa Associated with Human Fungal Black-Grain Mycetomas: Emarellia grisea gen. nov., sp. nov., and Emarellia paragrisea sp. nov. – Andrew M. Borman – Journal of Clinical Microbiology

Sociomicrobiology and Pathogenic Bacteria – Joao B. Xavier – Microbiology Spectrum

Paleomicrobiology Data: Authentification and Interpretation – Michel Drancourt – Microbiology Spectrum

Animal experiments

Dietary fucoidan modulates the gut microbiota in mice by increasing the abundance of Lactobacillus and Ruminococcaceae – Qingsen Shang – Food & Function

Animal microbiome

Perspective: Corals’ microbial sentinels – Tracy D. Ainsworth – Science

Plant, root, and soil microbiome

Escaping Underground Nets: Extracellular DNases Degrade Plant Extracellular Traps and Contribute to Virulence of the Plant Pathogenic Bacterium Ralstonia solanacearum – Tuan Minh Tran – PLOS Pathogens

Press: An ‘arms race’ raging beneath our plants: A crop’s DNA-laden root trap manages to hold on to only a quarter of its bacterial prisoners. – Amy Middleton – Cosmos Magazine

Responsiveness of soil nitrogen fractions and bacterial communities to afforestation in the Loess Hilly Region (LHR) of China – Chengjie Ren – Scientific Reports

Spatial Shifts in Soil Microbial Activity and Degradation of Pasture Cover Caused by Prolonged Exposure to Cement Dust – Fuensanta Caravaca – Land Degradation & Development

Water and extremophile microbiome

Biogeochemical and 16S rRNA gene sequence evidence supports a novel mode of anaerobic methanotrophy in permanently ice-covered Lake Fryxell, Antarctica – Matthew A. Saxton – Limnology and Oceanography

Food microbiology

The Microbiome and Metabolites in Fermented Pu-erh Tea as Revealed by High-Throughput Sequencing and Quantitative Multiplex Metabolite Analysis – Yongjie Zhang – PLOS ONE

More microbiology

Sugar Synthesis from CO2 in Escherichia coli – Niv Antonovsky – Cell

Press: Eating air, making fuel. Scientists engineer bacteria to create sugar from the greenhouse gas carbon dioxide – Science Daily

Not a scientific paper, just a list of links: Web Alert: Synthetic microbial communities: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology – Lawrence P. Wackett – Environmental Microbiology

Techniques

High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy – Yuichiro Nishimoto – Gut

Microbes in the news

New life form discovered in saliva is linked to human disease – Andy Coghlan – New Scientist

Seagulls Are Carrying a Dangerous Superbug Through the Skies – Maryn McKenna – National Geographic
Beware of Seagulls Carrying This Dangerous Superbug – Laura Lorenzetti – Fortune

Microbes In The Body Affect Success Of Organ Transplants: Study – Katrina Pascual -Tech Times

Scientists just found a compound that kills 98% of a drug-resistant bacteria – Fiona MacDonald – Science Alert

Milken Institute School of Public Health researchers awarded $7 million to study microbiome – Sera Royal – The GW Hatchet

Mycobacterium in olive oil for cancer treatment – EurekAlert

Scientists discover unsuspected bacterial link to bile duct cancer – MedicalXpress

Bik’s completely-not-microbiology Picks

The social dilemma of autonomous vehicles – Jean-François Bonnefon – Science

June 23, 2016

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Red snow microbiomes and melting glaciers, effect of earthworms on microbes, microbiome in COPD.

Pregnancy and birth

Early Gut Microbiota Perturbations Following Intrapartum Antibiotic Prophylaxis to Prevent Group B Streptococcal Disease – Giuseppe Mazzola – PLOS ONE

Human respiratory microbiome

Editorial: Early life nasal microbiota in infants with cystic fibrosis – Fiona J Whelan – The Lancet Respiratory Medicine

Review: Understanding the role of the microbiome in COPD: Principles, Challenges and Future Directions – Yvonne J. Huang – Translational Research

Human gut microbiome

Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition – Maryam Tidjani Alou – Anaerobe

Review: Understanding the mechanisms of faecal microbiota transplantation – Alexander Khoruts – Nature Reviews Gastroenterology & Hepatology

Review: Microbe-host interactions: Influence of the gut microbiota on the enteric nervous system – Niall P. Hyland – Developmental Biology

Systematic review: Probiotic supplementation can positively affect anxiety and depressive symptoms: a systematic review of randomized controlled trials – Meysam Pirbaglou – Nutrition Research

Animal experiments

Maternal gut and fetal brain connection: Increased anxiety and reduced social interactions in Wistar rat offspring following peri-conceptional antibiotic exposure – Stéphanie Degroote – Progress in Neuro-Psychopharmacology and Biological Psychiatry

A human gut ecosystem protects against C. difficile disease by targeting TcdA – Sarah Lynn Martz – Journal of Gastroenterology

Animal microbiome

Species-specific effects of earthworms on microbial communities and the fate of litter-derived carbon – Chih-Han Chang – Soil Biology and Biochemistry

Diversity of natural product biosynthetic genes in the microbiome of the deep sea sponges Inflatella pellicula, Poecillastra compressa and Stelletta normani – Alan D. Dobson – Frontiers in Microbiology

Plant, root, and soil microbiome

Tree species select diverse soil fungal communities expressing different sets of lignocellulolytic enzyme-encoding genes – Florian Barbi – Soil Biology and Biochemistry

Repeated annual glyphosate applications may impair beneficial soil microorganisms in temperate grassland – M. Druille – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

 The biogeography of red snow microbiomes and their role in melting arctic glaciers – Stefanie Lutz – Nature Communications

Press: The Arctic’s pretty but alarming strawberry-pink snow – Ben Guarino – Washington Post
This Pink Snow Does Not Bode Well For Our Future – Maddie Stone – Gizmodo

Effects of heap-bioleaching plant on microbial community of the nearby river – Mingjiang Zhang – International Biodeterioration & Biodegradation

Molecular Characterization of Aquatic Bacterial Communities in Dinaric Range Caves – Pleše, Bruna – Water Environment Research

Air microbiome

High-throughput sequencing reveals unprecedented diversities of Aspergillus species in outdoor air – Seungeun Lee – Letters in Applied Microbiology

Food microbiology

Changes in the microbiota of lamb packaged in a vacuum and in modified atmospheres during chilled storage analysed by high-throughput sequencing – Taojun Wang – Meat Science

Microbial Diversity of Type I Sourdoughs Prepared and Back-Slopped with Wholemeal and Refined Soft (Triticum aestivum) Wheat Flours – Manuela Taccari – Journal of Food Science

Added ingredients affect the microbiota and biochemical characteristics of durum wheat type-I sourdough – Fabio Minervini – Food Microbiology

Fungal diversity and ecosystem function data from wine fermentation vats and microcosms – Primrose J. Boynton – Data in Brief

The phenotypic characterization of yeast strains to stresses inherent to wine fermentation in warm climates – M. García – Journal of Applied Microbiology

Built environment microbiology

Contamination of healthcare workers’ mobile phones by epidemic viruses – S. Pillet – Clinical Microbiology and Infection

Press: Mobile devices of healthcare workers often contaminated by viral RNA – News Medical

No access for me, but intriguing title: Show research into the human microbiome can be used to solve crimes – Kyle Nothern – Southern California Interdisciplinary Law Journal

Microbes in the news
Video: Citizen Science and Mapping the Microbiome – Eric J. Topol interviews Jessica Richman – Medscape

Mapping the subway’s microbiome. Barcelona takes part in the international research project Metasub, which aims to map the microbiome of public transit systems in 54 cities worldwide – EurekAlert

Biology professor helps author free textbook, saving students hundreds: OpenStax Microbiology – Lainie Mazzullo – Wichita State University

Science, publishing, and career

At 31, she runs one of the hottest biotech companies in the country, with Rachel Haurwitz, CEO of Caribou Biosciences – Andrew Joseph – STAT news

Stem cell scientist Paolo Macchiarini suspected of involuntary manslaughter – STAT news

June 22, 2016

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Nipple aspirate, CNS infections, fiber and food allergies, horses and honeybee bacteria, and a report from the subway citizen science project.

General human microbiome

Commentary: Lessons Learned from Probing for Impacts of Triclosan and Triclocarban on Human Microbiomes – Rolf U. Halden – mSphere

Human nipple microbiome

Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors – Alfred A. Chan – Scientific Reports

Human vaginal microbiome

Impact of Probiotic SYNBIO® Administered by Vaginal Suppositories in Promoting Vaginal Health of Apparently Healthy Women – Maria Cristina Verdenelli – Current Microbiology

Human gut microbiome

Alterations of Intestinal Microbiome by Antibiotic Therapy in Hospitalized Children – Miriam R. Fernandes – Microbial Drug Resistance

Could gut microbiota serve as prognostic biomarker associated with colorectal cancer patients’ survival? A pilot study on relevant mechanism – Zhiliang Wei – Oncotarget

ASM Microbe 2016 abstract: Increased Akkermansia muciniphila and Bacteroides fragilis Group Abundance After Islamic Fasting – C. Erdogdu – ASM Microbe 2016

Press: Happy Ramadan From Your Microbiome! – Gastroenterology & Endoscopy News

Review: Inflammation and the microbiome: implications for depressive disorders – Shawn Hayley – Current Opinion in Pharmacology

Review: Role of the microbiome, probiotics, and ‘dysbiosis therapy’ in critical illness.– Wischmeyer, Paul E. – Current Opinion in Critical Care

Infection and microbiology

Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system – Steven L. Salzberg – Neurology Neuroimmunology & Neuroinflammation

Press: Diagnosing brain infections using metagenomics – Julian Harris – PHG Foundation

Animal experiments

Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways – Jian Tan – Cell Reports

Press: Diet high in fiber and vitamin A key to preventing allergies to peanuts and other triggers – EurekAlert

Gut microbiota translocation to the pancreatic lymph nodes triggers NOD2 activation and contributes to T1D onset – Frederico R.C. Costa – Journal of Experimental Medicine

Cutting Edge: Commensal Microbiota Has Disparate Effects on Manifestations of Polyglandular Autoimmune Inflammation – Camilla H. F. Hansen – The Journal of Immunology

Fighting Off Wound Pathogens in Horses with Honeybee Lactic Acid Bacteria – Tobias C. Olofsson – Current Microbiology

Plant, root, and soil microbiome

Local diversity of heathland Cercozoa explored by in-depth sequencing – Christoffer Bugge Harder – the ISME Journal

Press: Immense species richness of bacterial-eating microorganisms discovered in soil – Phys.org

Characterization of cadmium-resistant bacteria and their potential for reducing accumulation of cadmium in rice grains – Xiaoyan Lin – Science of The Total Environment
Editorial special issue: Soil, plants and endophytes – Stéphane Compant – Plant and Soil

Water and extremophile microbiome

Diverse Sulfur Metabolisms from Two Subterranean Sulfidic Spring Systems – Karen Rossmassler – FEMS Microbiology Letters

Metabolic potential of microbial mats and microbialites: autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources – Daniel Cerqueda-García – Journal of Bioinformatics and Computational Biology

Waste and pollution microbiology

Microbial contamination along the main open wastewater and storm water channel of Hanoi, Vietnam, and potential health risks for urban farmers – Samuel Fuhrimann – Science of The Total Environment

Isolation of Bdellovibrio bacteriovorus from a tropical wastewater treatment plant and predation of mixed species biofilms assembled by the native community members – Shugeng Feng – Environmental Microbiology

Microbial forensics

Microbial forensics: next‐generation sequencing as catalyst – Irene Kuiper – EMBO Reports

Bioinformatics and metagenomics

MEGAN Community Edition – Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data – Daniel H. Huson – PLOS Computational Biology

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses – François Enault – The ISME Journal

More microbiology

Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing – Justin Jee – Nature

Press: Sequencing method precise enough to reveal mechanisms by which bacteria resist antibiotics – Phys.org

Darwinolide, a New Diterpene Scaffold That Inhibits Methicillin-Resistant Staphylococcus aureus Biofilm from the Antarctic Sponge Dendrilla membranosa – Jacqueline L. von Salm – Organic Letters

Press: Antibiotics from a Sponge. Could a new compound from Antarctic sea sponges be the key to breaching MRSA’s impregnable barricades? – Michael Lucibella – Antarctic Sun

Microbes in the news

MetaSUB Citizen Science Project:
With video of researchers swabbing away: Biologists Study What Kind Of Bacteria Is On New York City Subways – CBS Local
Qiagen, CosmosID Join International Urban Microbiome Project – Genome Web

New Life Found That Lives Off Electricity. Scientists have figured out how microbes can suck energy from rocks. Such life-forms might be more widespread than anyone anticipated – Emily Singer – Quanta Magazine

High-tech program on microbiome-based research launched in Qingdao – Hu Qing – China Daily

Explained: flesh eating bacteria in the Gulf of Mexico – Dylan Baddour – Houston Chronicle

Science, publishing, and career

Your Science Conference Should Have a Code of Conduct – Brett Favaro – Frontiers in Marine Science

Science in China – A special issue looks at the country’s astonishing scientific trajectory as it seeks to secure its spot among the leaders in innovation – Nature
China by the numbers. Research capacity has grown rapidly, and now quality is on the rise – Richard Van Noorden – Nature

Global Research Council: Commit to equity for women researchers – France A. Córdova – Nature

June 21, 2016

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An invertebrate gets its amino acids from microbial symbionts, microbiota and allograft rejection, high-altitude Andes lakes, and determining absolute microbiota abundances by spiking-in bacteria.

Jobs and events

Postdoctoral Researcher Microbial Ecology & Bioinformatics – NIOO-KNAW, WUR, Wageningen, The Netherlands

Report from the Microbiome R&D and Business Collaboration Forum, April 11–12, 2016, London, UK – Duc H. Le – EBioMedicine

General microbiome

Review: Diversity at low abundance: The phenomenon of the rare bacterial biosphere – M. Yu. Skopina – Microbiology

Workshop report: Culture-Independent Diagnostics for Health Security – Doggett Norman A.- Health Security

Viewpoint: Addressing Infectious Disease Challenges by Investigating Microbiomes – Emily P. Balskus – ACS Infectious Diseases

Human oral microbiome

Molecular analysis of fungal populations in patients with oral candidiasis using next-generation sequencing – Yumi Imabayashi – Scientific Reports

Human reproductive tract microbiome

Review: Chlamydia trachomatis Genital Tract Infections: When Host Immune Response and the Microbiome Collide – Noa Ziklo – Trends in Microbiology

Human gut microbiome

Review: Microbes, Immunity and Behaviour: Psychoneuroimmunology Meets the Microbiome – Timothy G Dinan – Neuropsychopharmacology

Review: Emerging roles for antigen presentation in establishing host–microbiome symbiosis – Nicholas J. Bessman – Immunological Reviews

Book Chapter: The Effect of H. pylori Infection on the Gastric Microbiota – Hyun Jin Jo – Helicobacter Pylori (Springer book)

Animal and in vitro experiments

The composition of the microbiota modulates allograft rejection – Yuk Man Lei – The Journal of Clinical Investigation

Press: Microbiota affect the rate of transplant acceptance and rejection – MedicalXpress

Maternal Metabolic Syndrome Programs Mitochondrial Dysfunction via Germline Changes across Three Generations – Jessica L. Saben – Cell Reports

Press, extrapolated conclusion: Obese Pregnant Women With Poor Diets May Worsen The Childhood Obesity Epidemic: Study – Samantha Olson – Medical Daily

Diet-dependent, microbiota-independent regulation of IL-10-producing lamina propria macrophages in the small intestine – Takanori Ochi – Scientific Reports

Characterization of Cimex lectularius (bedbug) defensin peptide and its antimicrobial activity against human skin microflora – Akanksha Kaushal – Biochemical and Biophysical Research Communications

Variability of arsenic bioaccessibility and metabolism in soils by human gut microbiota using different in vitro methods combined with SHIME – Naiyi Yin – Science of The Total Environment

Transient activation of mucosal effector immune responses by resident intestinal bacteria in normal hosts is regulated by interleukin-10 signalling – Cong Wu – Immunology

Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community – Prabhakar D. Pandit – Bioresource Technology

Review: Strategies to modulate the intestinal microbiota of Tilapia (Oreochromis sp.) in aquaculture: a review – Alyssa M. Haygood – Reviews in Aquaculture

Animal microbiome

Seasonality and Locality Affect the Diversity of Anopheles gambiae and Anopheles coluzzii Midgut Microbiota from Ghana – Jewelna Akorli – PLOS ONE

A Nightmare for Males? A Maternally Transmitted Male-Killing Bacterium and Strong Female Bias in a Green Lacewing Population – Masayuki Hayashi – PLOS ONE
http://journals.plos.org/plosone/article?

Testosterone levels are positively correlated with cloacal bacterial diversity and the relative abundance of Chlamydiae in breeding male rufous-collared sparrows
– Camilo Escallón – Functional Ecology

The dominant detritus-feeding invertebrate in arctic peat soils derives its essential amino acids from gut symbionts – Thomas Larsen – Journal of Animal Ecology

Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod Bathynomus sp – Yong Wang – Environmental Microbiology

Review: Is gastrointestinal microbiota relevant for endogenous mercury methylation in terrestrial animals? – R.C. Rodríguez Martín-Doimeadios – Environmental Research

Plant, root, and soil microbiome

Multi-targeted metagenetic analysis of the influence of climate and environmental parameters on soil microbial communities along an elevational gradient – Anders Lanzén – Scientific Reports

Integrated analysis of root microbiomes of soybean and wheat from agricultural fields – Nicolás Rascovan – Scientific Reports

Dark stains on rock surfaces in Driny Cave (Little Carpathian Mountains, Slovakia)
Rafał Ogórek – Extremophiles

Water and extremophile microbiome

Diversity of extremophilic bacteria in the sediment of high-altitude lakes located in the mountain desert of Ojos del Salado volcano, Dry-Andes – Júlia Margit Aszalós – Extremophiles

Microbial interactions lead to rapid micro-scale successions on model marine particles –
Manoshi S. Datta – Nature Communications

Bacteriophages in Arctic and Antarctic low-temperature systems – S. N. Filippova – Microbiology

Diversity of methanogenic archaea from the 2012 terrestrial hot spring (Valley of Geysers, Kamchatka) – A. Y. Merkel – Microbiology

Comparative analysis of prokaryotic diversity in solar salterns in eastern Anatolia (Turkey) – Seval Çınar – Extremophiles

Techniques

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria – 
Frank Stämmler – Microbiome

Metagenomics and bioinformatics

Data Labours: How the Sequence Databases GenBank and EMBL-Bank Make Data – Tahani Nadima – Science as Culture

Principle, analysis, application and challenges of next-generation sequencing: a review – Khalid Raza – arXIv

Microbes in the news

Does a pipette work in space? with NASA Astronaut Dr Kate Rubins – Microbe Talk – Microbe Post

An Antarctic sponge offers new hope against deadly MRSA infection – Matt Windsor – UAB

Dental Microbes Not All in the Family. Kids often acquire cavity-causing bacteria from non-family members, researchers report at the American Society for Microbiology annual meeting – Tanya Lewis – The Scientist

Never-Before Human-Detected, Potentially Pathogenic Bacterium Found in Children With Acute Leukemia Human Microbiology Institute investigates potential role of previously unknown bacteria – PR Newswire

Geisinger’s Donna Wolk recognized for work in microbiology – Daily Item

Microbial mass extinctions were kicked off by human evolution – Andy Coghlan – New Scientist

Global Microbiome Initiative Explores Subways for Drug-Resistance Markers:
MetaSUB Consortium will collect DNA and RNA samples from high-traffic areas in subway systems, buses, and parks in 54 cities worldwide – GenEngNews

June 20, 2016

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The temperate tree phyllosphere, Qaanaaq Glacier, effect of human activities on Hong Kong coast microbes, and genome assembly from read clouds.

Events

Microbiome R&D and Business Collaboration Forum: USA, October 3-4, San Diego

Pregnancy and birth

Putative periodontopathic bacteria and herpesviruses in pregnant women: a case-control study – Haixia Lu – Scientific Reports

Human gut microbiome

Letter to Editor: Reduction of antibiotic resistance genes in intestinal microbiota of recurrent Clostridium difficile patients after fecal microbiota transplantation – Hanne Jouhten – Clinical Infectious Diseases Advance Access

Review: The Gut Microbiota and Inflammatory Bowel Diseases – Jun Miyoshi – Translational Research

Review: Links Between the Microbiome and Bone – C.J. Hernandez – Journal of Bone and Mineral Research

Animal models

Interactions between the colonic transcriptome, metabolome and microbiome in mouse models of obesity-induced intestinal cancer – Anna C. Pfalzer – Physiological Genomics

Plant, root, and soil microbiome

Host species identity, site and time drive temperate tree phyllosphere bacterial community structure – Isabelle Laforest-Lapointe – Microbiome

Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations – Quan Li – Scientific Reports

A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan – E. V. Pershina – Eurasian Soil Science

A novel isolate and widespread abundance of the candidate alphaproteobacterial order (Ellin 329), in southern Appalachian peatlands – Austin B. Harbison – FEMS Microbiology Letters

Water and extremophile microbiome

Microbial community variation in cryoconite granules on Qaanaaq Glacier, NW Greenland – Jun Uetake – FEMS Microbiology Ecology

Mechanisms driving Antarctic microbial community responses to ocean acidification: a network modelling approach – Roshni C. Subramaniam – Polar Biology

Video article: Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR – Enrico Tatti – Journal of Visualized Experiments

Waste and pollution microbiology

Microorganisms in heavy metal bioremediation: strategies for applying microbial-community engineering to remediate soils – Jennifer L. Wood – AIMS Bioengineering

Impacts of Human Activities on Distribution of Sulfate Reducing Prokaryotes and Antibiotic Resistance Genes in Marine Coastal Sediments of Hong Kong – Feng Guo – FEMS Microbiology Ecology

Shotgun metagenomic profiles have a high capacity to discriminate activated sludge according to wastewater type – Federico M. Ibarbalz – Applied and Environmental Microbiology

Characteristics of Sediment Bacterial Community in Response to Environmental Impacts in a Sewage Polluted River – Jialin Li – Journal of Coastal Research

Plants rather than mineral fertilization shape microbial community structure and functional potential in legacy contaminated soil – Jakub Ridl – Frontiers in Microbiology

Food microbiology

Viable bacterial population and persistence of foodborne pathogens on the pear carpoplane – Francois J. Duvenage – Journal of the Science of Food and Agriculture

Book: Acetic Acid Bacteria: Ecology and Physiology – Springer

Metagenomics and bioinformatics

Genome assembly from synthetic long read clouds – Volodymyr Kuleshov – Bioinformatics

Unsupervised Binning of Metagenomic Assembled Contigs Using Improved Fuzzy C-Means Method – Yun Liu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Bioreactor microbiology

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion – Inka Vanwonterghem – Environmental Microbiology

Microbes in the news

From ASM Microbe 2016: Bacteria Can Persist on Gloves, Transfer to Surfaces – Neil Osterweil – Medscape

Ischemic stroke therapy – does the gut microbiota hold the key? – Sara Adães – PLOS Neuro Community

French microbiologist hopes CRISPR/Cas9 can be used medically, with Emmanuelle Charpentier – Focus Taiwan

Chipotle Bosses Accused Of Insider Trading During Bacteria Scandals – Scott Heins – Gothamist

Bik’s Not-Microbiology Picks

Why Did Scientists Release Dead Sea Turtles into Chesapeake Bay? – Erica Tennenhouse – The Science Explorer

June 18, 2016

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Your Saturday Microbiome Digest: CSF metagenomics in multiple sclerosis, Caenorhabditis elegans responses to bacteria, and archaeal communities in permafrost.

Infection and microbes

Only microbial contamination found: Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis – Karol Perlejewski – Advances in Experimental Medicine and Biology

Review: The regulation of host defences to infection by the microbiota – Rebecca L. Brown – Immunology

Animal and in vitro experiments

Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation – Aaron W. Miller – Microbial Ecology

Differential Utilization of Basic Proline-Rich Glycoproteins During Growth of Oral Bacteria in Saliva – Yuan Zhou – Applied and Environmental Microbiology

Caenorhabditis elegans responses to bacteria from its natural habitats – Buck S. Samuel – PNAS

Plant, root, and soil microbiome

Presence and persistence of viable, clinically relevant Legionella pneumophila bacteria in garden soil in the Netherlands – E. van Heijnsbergen – Applied and Environmental Microbiology

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons – C. Ryan Pento – Frontiers in Microbiology

Monitoring fungi in ecological restorations of coastal Indiana, U.S.A. – Peter G. Avis – Restoration Ecology

Review: Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing “Stress-on-Stress” Responses – Hamed Azarbad – MDPI International Journal of Molecular Sciences

Water and extremophile microbiome

Archaeal communities of Arctic methane-containing permafrost – Victoria Shcherbakova – FEMS Microbiology Ecology

Microbial community diversity, structure, and assembly across oxygen gradients in meromictic marine lakes, Palau – Matthew S. Meyerhof – Environmental Microbiology

Bioreactor microbiology

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant – Vera Ortseifen – Journal of Biotechnology

Bioinformatics

Finds microbial interactions based on PubMed abstracts, so basically finding interactions that were already published (???): @MInter: Automated Text-mining of Microbial Interactions – Lim Kun Ming Kenneth – Bioinformatics

More microbiology

In situ replication rates for uncultivated bacteria in microbial communities – Christopher T Brown – bioRxiv

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities – Sebastian Germerodt – PLOS Computational Biology

Microbes in the news

UWM professor taking a deeper dive on beach pollution data – Milwaukee-Wisconsin Journal Sentinel

The medical revolution that delves into humans’ inner aliens – Robert Matthews – The National

Brewing on the wild side: IU’s Dr. Matthew L. Bochman – Rita Kohn – Nuvo.net

Fecal bacteria and antibiotic resistance genes found in water samples from fly-in Northern Manitoba – Ian Graham – Thompson Citizen

CosmosID, BioCollective Collaborate on Microbiome Analysis Kit – GenomeWeb

June 17, 2016

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Gastric bypass induces persistent gut microbiome changes, omnivorous lizards going vegetarian, new Borrelia species in Australian ticks, a free-living Bradyrhizobium, plant responses to phyllosphere commensals, and chemotrophic microbial populations in Yellowstone hot springs.

Events

HT: Jonathan Eisen: June 20-21 Meeting #2 for NAS Microbiomes of the Built Environment Study. Click here to register for the webcast (free!).

Human respiratory microbiome

Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children – Marcos Pérez-Losada – Microbiome

Human gut microbiome

Antibiotic-induced gut microbiota disruption during human endotoxemia: a randomised controlled study – Jacqueline M Lankelma – Gut
Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota – Albert Palleja – Genome Medicine

Review: Metabolomics of autism spectrum disorders: early insights regarding mammalian-microbial cometabolites – Michele Mussap – Expert Review of Molecular Diagnostics

Review: How the microbiota shapes rheumatic diseases – Tom Van de Wiele – Nature Reviews Rheumatology

Animal and other experiments

Physiological and microbial adjustments to diet quality permit facultative herbivory in an omnivorous lizard – Kevin D. Kohl – Journal of Experimental Biology

Press: How does a lizard go vegetarian? By growing its gut – Patrick Monahan – Science Magazine

Nasal commensal Staphylococcus epidermidis counteracts influenza virus – Hui-Wen Chen – Scientific Reports

Animal microbiome

Diversity, structure and convergent evolution of the global sponge microbiome – Torsten Thomas – Nature Communications

Does canine inflammatory bowel disease influence gut microbial profile and host metabolism? – Jia Xu – BMC Veterinary Research

Novel Borrelia species detected in echidna ticks, Bothriocroton concolor, in Australia – Siew-May Loh – Parasites & Vectors

Press: New bacteria discovered in Australian ticks – MedicalXpress

Plant, root, and soil microbiome

Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes – a genome comparison – Frances Patricia Jones – Scientific Reports

Press: Study unlocks surprising behaviour of soil bacteria – Mark Kinver – BBC

The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health – Christine Vogel – New Phytologist

DNA from dust: comparative genomics of vaccine-break virus in the field – Utsav Pandey – bioRxiv

Water and extremophile microbiome

Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs – Daniel R. Colman – FEMS Microbiology Ecology

Large shifts among eukaryotes, bacteria, and archaea define the vertical organization of a lake sediment – Christian Wurzbacher – bioRxiv

Microbes in the news

Featuring an All Male Panel: That Gut Feeling: Part One. Dan Saladino discovers the world of the gut microbiota, the vast array of microbes within us all – BBC Radio

Bik’s Picks

Klinefelter’s syndrome (47,XXY) is in excess among men with Sjögren’s syndrome –
Valerie M. Harris – Clinical Immunology

Press: Does X mark the spot? A new clue why autoimmune diseases target women – Oklahoma Medical Research Foundation

June 16, 2016

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ASM Microbe 2016 meeting Tweet-up, two exciting papers on infant gut colonization, Lactobacillus reuteri restores autism-like behavior in a mouse model, rumen microbiomes in high-altitude mammals, an undergraduate lab in food spoilage, the archaeal origins of eukaryotes, and the discovery of CRISPRs.

Events

ASM Microbe 2016 Tweet-up is Friday, June 17, 11:45-12:30 in the Peer-to-Peer Exchange Zone (in the Exhibition Hall)

Pregnancy and birth

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability – Moran Yassour – Science Translational Medicine

Antibiotics, birth mode, and diet shape microbiome maturation during early life – Nicholas A. Bokulic – Science Translational Medicine

Press: Antibiotics given to babies change their gut microbes for years – Anna Vlasits – STAT
Don’t Stress About Your Baby’s Microbiome Just Yet. Antibiotics and C-sections might change a baby’s microbes, but it’s not clear that those changes are bad, lasting, or that they matter at all. – Ed Yong- the Atlantic

Research Highlight: Growing up together — gut microbiota assembly and IgA – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Opinion: Why Don’t All Infants Have Bifidobacteria in Their Stool? – Gerald W. Tannock – Frontiers in Microbiology

Human oral microbiome
A preliminary study of the oral microbiota in Chinese patients with Sjögren’s Syndrome – Miaoran Li – Archives of Oral Biology

Detection of Novel Integrons in the Metagenome of Human Saliva – Supathep Tansirichaiya – PLOS ONE

Human respiratory microbiome

Severe Achromobacter xylosoxidans infection and loss of sputum bacterial diversity in an adult patient with cystic fibrosis – Nick P. Talbot – Paediatric Respiratory Reviews

Human gut microbiome

Occurrence of human sapoviruses in wastewater and stool samples in Rio de Janeiro, Brazil – Julia Monassa Fioretti – Journal of Applied Microbiology

Review: Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism – Annika Wahlström – Cell Metabolism

Review: Repertoire of human gut microbes – Perrine Hugon – Microbial Pathogenesis

Review: The intestinal microbiome and surgical disease – Monika A. Krezalek – Current Problems in Surgery

Animal experiments

Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring – Shelly A. Buffington – Cell

Press: A single species of gut bacteria can reverse autism-related social behavior in mice – MedicalXpress
Single Bacterial Species Improves Autism-Like Behavior in Mice – Ruth Williams – The Scientist

Absence of gut microbiota influences lipopolysaccharide-induced behavioral changes in mice – Alline C. Campos – Behavioural Brain Research

Altered Microbiota Contributes to Reduced Diet-Induced Obesity upon Cold Exposure –
Marika Ziętak – Cell Metabolism

Revealing the combined effects of lactulose and probiotic enterococci on the swine faecal microbiota using 454 pyrosequencing – Jong Pyo Chae – Microbial Biotechnology

Lactobacillus rhamnosus GG modulates innate signaling pathway and cytokine responses to rotavirus vaccine in intestinal mononuclear cells of gnotobiotic pigs transplanted with human gut microbiota – Haifeng Wang – BMC Microbiology

Effect of postnatal low-dose exposure to environmental chemicals on the gut microbiome in a rodent model – Jianzhong Hu – Microbiome

Animal microbiome

Multiyear Survey of Coccidia, Cryptosporidia, Microsporidia, Histomona, and Hematozoa in Wild Quail in the Rolling Plains Ecoregion of Texas and Oklahoma, USA – Lixin Xiang – The Journal of Eukaryotic Microbiology

Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals – Zhigang Zhang – Current Biology

Plant, root, and soil microbiome

Biogeographical patterns in fungal communities from soils cultivated with sugarcane – Thiago Gumiere – Journal of Biogeography

Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities – S. Uroz – Scientific Reports

Inoculant of Arbuscular Mycorrhizal Fungi (Rhizophagus clarus) Increase Yield of Soybean and Cotton under Field Conditions – Martha V. T. Cely – Frontiers in Microbiology

Patterns and drivers of soil microbial communities in Tibetan alpine and global terrestrial ecosystems – Yong-Liang Chen – Journal of Biogeography

Water and extremophile microbiome

Microbial Inventory of Deeply Buried Oceanic Crust from a Young Ridge Flank – Steffen L. Jørgensen – Frontiers in Microbiology

Resilience of Freshwater Communities of Small Microbial Eukaryotes Undergoing Severe Drought Events – Marianne Simon – Frontiers in Microbiology

Food microbiology

Undergraduate Laboratory Exercises Specific to Food Spoilage Microbiology – Abigail B. Snyder – Journal of Food Science Education

Waste and pollution microbiology

Comparison of microbial taxonomic and functional shift pattern along contamination gradient – Youhua Ren – BMC Microbiology

More microbiology

On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype: A Hunt for the Archaeal Ancestor of Eukaryotes – Gautam Dey – Trends in Cell Biology

Press: Life as we know it most likely arose via ‘long, slow dance’ – EurekAlert

Mentions our Mycobacterium paper from 1991! The discovery of CRISPR in archaea and bacteria – Francisco J. M. Mojica – The FEBS Journal

Microbes in the news

Antibiotics increase availability of nutrients in the gut, enabling growth of pathogens, with Franziska Faber – UC Davis – Science Daily

Whole Foods Must Clean Up Its Act, FDA Says. Agency warns of ‘serious violations’ at food-preparation plant – Jesse Newman and Heather Haddon – Wall Street Journal

The Parasite Underground – A shadow network of patients are trying to treat their own debilitating diseases — by infecting themselves with gastrointestinal worms – Moises Velasquez-Manoff – The New York Times Magazine

uBiome Doubles Research Grant to Award Two Microbiome Researchers up to $100,000 Each – PR Web

About MetaFast: Personalized medicine will employ computer algorithms – Science Daily

University Seeks to Capitalize on Push to Harness Helpful Microbes – In more recent years, microbes have proved their worth through things like polymerase chain reaction – Terry Devitt – University of Wisconsin-Madison

TGen test shows promise for diagnosing Lyme – Emery Cowan – AZ Daily Sun

Important opinion piece: We are not viruses: Don’t limit gay men from donating blood – Benjamin Mazer – STAT news

Satire: New Mountain Dew Vows To Kill 99.9% Of Stomach Bacteria – The Onion

Science, publishing, and career

A peek at peer review helps young scientists – Jeffrey Mervis – Science

The age of the Twitter conference – Stephanie Avery-Gomm – Science