Category Archives: Metabolomics

March 30, 2016

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Microbiome and mood, bone marrow transplantation, archaea in kangaroos, tardigrade genome contamination.

Events

UC Berkeley Event: Archaea and the Three Domains: Classification of Life for Middle School

Microbiome expert to speak at UB –  Martin Blaser is a former president of the Infectious Diseases Society of America, April 6-7 – Charlotte Hsu – University of Buffalo

Pregnancy and birth

Microbiome: Antibiotics and the infant microflora – Kristen Meyer & Kjersti Aagaard – Nature Microbiology

Human mouth microbiome

Accuracy of commercial kits and published primer pairs for the detection of periodontopathogens – Elisabeth Santigli – Clinical Oral Investigations

Human gut microbiome

Gut microbes in correlation with mood: case study in a closed experimental human life support system – L. Li – Neurogastroenterology & Motility

Anti-TNF Therapy Response in Patients with Ulcerative Colitis Is Associated with Colonic Antimicrobial Peptide Expression and Microbiota Composition – Maria K. Magnusson – Journal of Crohn’s and Colitis

Gut microbiota profiling of pediatric NAFLD and obese patients unveiled by an integrated meta-omics based approach – Federica Del Chierico – Hepatology

Commentary: Role of gut flora after bone marrow transplantation – Jonathan U. Peled – Nature Microbiology

Animal microbiome

Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids – Emily C Hoedt – The ISME Journal

Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater – Eleni Voudanta – PeerJ

Plant, root, and soil microbiome

Tobacco, Microbes, and Carcinogens: Correlation Between Tobacco Cure Conditions, Tobacco-Specific Nitrosamine Content, and Cured Leaf Microbial Community – Audrey D. Law – Microbial Ecology

Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland – Noriko A. Cassman – Scientific Reports

Drinking water microbiome

Flow cytometric examination of bacterial growth in a local drinking water network –
Sam Van Nevel – Water and Environment Journal

Animal microbiome

Breakdown of coevolution between symbiotic bacteria Wolbachia and their filarial hosts – Emilie Lefoulon – PeerJ

Built environment microbiome

Review (but did not make much sense to me): Toward a microbial Neolithic revolution in buildings – David S. Thaler – Microbiome

Bioreactor microbiome

Functional maintenance and structural flexibility of microbial communities perturbed by simulated intense rainfall in a pilot-scale membrane bioreactor – Yuya Sato – Applied Microbiology and Biotechnology

Fungi

News: Microbiology: Fungus produces a toxic surprise – Aaron P. Mitchell – Nature

Candidalysin is a fungal peptide toxin critical for mucosal infection – David L. Moyes – Nature

Biofilms

Spatio-temporal assembly of functional mineral scaffolds within microbial biofilms – Yaara Oppenheimer-Shaanan – NPJ Biofilms

Metagenomics and bioinformatics

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies – Tom O Delmont – PeerJ

myPhyloDB: a local web server for the storage and analysis of metagenomic data – Daniel K. Manter – Database

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning – Brian Cleary – Nature Biotechnology

Metabolomics

Optimization of metabolomics of defined in vitro gut microbial ecosystems – Dirk K. Wissenbach – International Journal of Medical Microbiology

Microbial ecology

Review: Challenges in microbial ecology: building predictive understanding of community function and dynamics – Stefanie Widder – The ISME Journal

Microbes in the news

Another reason to break the habit: Smoking alters bacterial balance in mouth – EurekAlert

Pseudomonas aeruginosa in shampoos and shower gels made by Gilchrist and Soames – FDA warning letter

Acne bacteria and hot dog cookers: Science projects take center stage at regional fair – Matt Barney – The Joplin Globe

Cave bacteria could control superbugs – News24

The 8-Bit Game That Makes Statistics Addictive – Ed Yong – The Atlantic

Microbes and art

“World’s First” Bacteria-Grown Book Combines Science and Culture – Nathaniel Ainley – The Creators Project

WTF

Polish company to brew beer from Czech model’s vagina bacteria – Ben Hooper – UPI

First Vaginal Beer: Bottled Instinct – Wojciech Mann – IndieGoGo
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March 17, 2016

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Metagenomics of Necrotizing Enterocolitis, sinus irrigation, variation in mice in German facilities, and bacteria vs phage.

Pregnancy and birth

The maternal microbiota drives early postnatal innate immune development – Mercedes Gomez de Agüero – Science

Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants – Doyle V. Ward – Cell Reports

Human respiratory microbiome

Evaluation of bacterial transmission to the paranasal sinuses through sinus irrigation – Leah J. Hauser – International Forum of Allergy & Rhinology

Human gut microbiome

Fecal Microbiota Transplantation in Children: A Brief Review – Suchitra K Hourigan – Pediatric Research

Forum: Oscillospira: a Central, Enigmatic Component of the Human Gut Microbiota – Tom Konikoff – Trends in Microbiology

Commentary: Recognizing that the microbiome is part of the human immune system will advance treatment of both cancer and infections – Richard L. Gallo – Journal of the American Academy of Dermatology

Review: Low calorie sweeteners and gut microbiota – Kristian Daly – Physiology & Behavior

Animal models

Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities – Philipp Rausch – International Journal of Medical Microbiology

Plant, soil, and root microbiome

Plant versus microbial controls on soil aggregate stability in a seasonally dry ecosystem – Joseph C. Blankinship – Geoderma

Soil microbial communities following bush removal in a Namibian savanna – Jeffrey S. Buyer – Soil

Monitoring benthic microflora in river bed sediments: a case study in the Anllóns River (Spain) – Diego Martiñá Prieto – Journal of Soils and Sediments

Biodiversity gradients in obligate symbiotic organisms: exploring the diversity and traits of lichen propagules across the United States – Erin A. Tripp – Journal of Biogeography

Viruses and phages

Classic Spotlight: Bacteria versus Phage—the Battle Rages! – Tina M. Henkin – Journal of Bacteriology

Techniques

Review: Confocal Microscopy Imaging of the Biofilm Matrix – Sebastian Schlafer – Journal of Microbiological Methods

Metabolomics

Optimization of Metabolomics of defined in vitro gut microbial ecosystems – Dirk K. Wissenbach – International Journal of Medical Microbiology

Review: Challenges of metabolomics in human gut microbiota research – Kirill S. Smirnov – International Journal of Medical Microbiology

Microbes in the News

Subset of E. coli bacteria linked to deadly disease in pre-term infants – Medical Xpress

Our gut microbiome is always changing; it’s also remarkably stable – Science Codex

Meeting report: Microbes in the City: Mapping the Urban Genome – New York Academy of Sciences

Viral Infections May Affect Cystic Fibrosis Patients’ Respiratory Microbiome, Study Says – Daniela Semedo – Lung Disease News

Diverse diets enrich gut microbes – Catharine Paddock – Medical News Today

Mother’s Microbiome Shapes Offspring’s Immunity – The maternal gut microbiome guides neo- and postnatal immune system development, a mouse study shows – Anna Azvolinsky – The Scientist

How bacteria get their magnetic compass – Robert Sanders – Berkeley News

Science, publishing, and career

Blogging for beginners – Andrew David Thaler – Science

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March 12, 2016

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Microbiomes of farmland frogs and grape vine, and functional structures in acid mine drainage microbes.

Human oral microbiome

Ecological changes in oral microcosm biofilm during maturation – Young-Seok Kim – Journal of Biomedical Optics

Human gut microbiome

Review: Consequences of bile salt biotransformations by intestinal bacteria – Jason M. Ridlon – Gut Micobes

Review: The microbiota–gut–brain axis and its potential therapeutic role in autism spectrum disorder – Q. Li,- Neuroscience

Animal models

Safety Evaluation of Neo Transgenic Pigs by Studying Changes in Gut Microbiota Using High-Throughput Sequencing Technology – Qingqing Wang – PLOS ONE

Animal microbiome

Changes of diet and dominant intestinal microbes in farmland frogs – Chun-Wen Chang – BMC Microbiology

Plant, soil, and microbiome

Vitis vinifera microbiome: from basic research to technological development – Cátia Pinto – BioControl

Water and extremophile microbiology

Predicting taxonomic and functional structure of microbial communities in acid mine drainage – Jialiang Kuang – The ISME Journal

Complete ecological isolation and cryptic diversity in Polynucleobacter bacteria not resolved by 16S rRNA gene sequences – Martin W Hahn – The ISME Journal

Waste and pollution microbiology

Changes of microbial composition during wastewater reclamation and distribution systems revealed by high-throughput sequencing analyses – Yiwen Lin – Frontiers of Environmental Science & Engineering

Metabolomics

Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease – Qiang Feng – Scientific Reports

Bioinformatics and metagenomics

Phylogeny-aware Identification and Correction of Taxonomically Mislabeled Sequences – Alexey M Kozlov – BioRxiv

Microbial Ecology

Challenges in microbial ecology: building predictive understanding of community function and dynamics – Widder, S – White Rose Research Online

Microbes in the news

A cloud of distinction – Could the trails of microbes we leave behind be used to solve crimes? Julian Smith picks up the scent – Julian Smith  – New Scientist

Stick Out Your Tongue: Citizen science project draws up the first oral microbiome map for the youth: Over 4,000 people have taken part in this hands-on scientific project in Barcelona- EurekAlert

Biologicals in quest for 2050: BioConsortia is evaluating microbes that could help protect seedlings emerging in cold and wet conditions. – AgriView

Gut Microbiome Analysis for Detecting Colon Cancer Mutations – Univesrity of Minnesota

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February 28, 2016

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Viral sequences in cancers, COPD, and EDGE, an easy online tool for metagenomics analysis.

Jobs

Researcher for a project on the effect of gut microbiome in human behavior – Radboud UMC Nijmegen, The Netherlands

General microbiome

Opinion: Manipulating Bacterial Communities by in situ Microbiome Engineering – Ravi U. Sheth – Trends in Genetics

Pregnancy and birth

Effect of Saccharomyces boulardii and Mode of Delivery on the Early Development of the Gut Microbial Community in Preterm Infants – Natalia Zeber-Lubecka – PLOS ONE

Human respiratory microbiome

Lung microbiome dynamics in chronic obstructive pulmonary disease exacerbations – Zhang Wang – European Respiratory Journal

Human gut microbiome

Presence of Porphyromonas gingivalis in esophagus and its association with the clinicopathological characteristics and survival in patients with esophageal cancer – Shegan Gao – BMC Infectious Agents and Cancer

Human colorectal mucosal microbiota correlates with its host niche physiology revealed by endomicroscopy – Ai-Hua Wang – Scientific Reports

Review: Gut Microbiota of Nonalcoholic Fatty Liver Disease – Reham M. Abdou – Digestive Diseases and Sciences

Review: Microbes and the Mind: Emerging Hallmarks of the Gut Microbiota-Brain Axis – Kylynda C. Bauer – Cellular Microbiology

Review: Beyond the gut bacterial microbiota: The gut virome – Paola Columpsi – Journal of Medical Virology

Human tissues and infection

Identification of Known and Novel Recurrent Viral Sequences in Data from Multiple Patients and Multiple Cancers – Jens Friis-Nielsen – MDPI Viruses

Models of microbiome research

Maternal Weaning Modulates Emotional Behavior and Regulates the Gut-Brain – Pamela Farshim – Scientific Reports

Rats: Correlations of Fecal Metabonomic and Microbiomic Changes Induced by High-fat Diet in the Pre-Obesity State – Hong Lin – Scientific Reports

Animal microbiome

18S rRNA V9 metabarcoding for diet characterization: a critical evaluation with two sympatric zooplanktivorous fish species – Aitor Albaina – Ecology and Evolution

Plant, root and soil microbiome

Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming – Kai Xue – Nature Climate Change

Online Springer Book: Microbial Inoculants in Sustainable Agricultural Productivity – Springer

Book chapter: Soil Effects of Genetically Modified Trees (GMTs) – Fernando Gallardo – Biosafety of Forest Transgenic Trees

Borderline Products between Bio-fertilizers/ Bio-effectors and Plant Protectants: The Role of Microbial Consortia – Marco Nuti – David Publishing Company

Differences in substrate use efficiency: impacts of microbial community composition, land use management, and substrate complexity – Tobias Bölscher – Biology and Fertility of Soils

Comparing how land use change impacts soil microbial catabolic respiration in Southwestern Amazon – Andre Mancebo Mazzetto – Brazilian Journal of Microbiology

Bacterial community dissimilarity between the surface and subsurface soils equals horizontal differences over several kilometers in the western Tibetan Plateau – Haiyan Chu – Environmental Microbiology

Soil and tree species traits both shape soil microbial communities during early growth of Chinese subtropical forests – Zhiqin Pei – Soil Biology and Biochemistry

Water and extremophile microbiome

Functional interactions of archaea, bacteria, and viruses in a hypersaline endolithic community – Alexander Crits-Christoph – Environmental Microbiology

Ecological succession leads to chemosynthesis in mats colonizing wood in sea water – Dimitri Kalenitchenko – The ISME Journal

Chapter One – Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes – M. Itävaara – Advances in Applied Microbiology

Waste and pollution microbiology

Bacterial ecology of abattoir wastewater treated by an anaerobic digestor – Linda Jabari – Brazilian Journal of Microbiology

High-Resolution Phylogenetic Analysis of Residual Bacterial Species of Fouled Membranes after NaOCl Cleaning – Ronald R. Navarro – Water Research

Microbial diversity and hydrocarbon degrading gene capacity of a crude oil field soil as determined by metagenomics analysis – Firouz Abbasian – Biotechnology Progress

Bioinformatics

Now peer reviewed: cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies – John H. Chase – mSystems

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation – Cecilia Noecker – mSystems

Assessing the performance of DNA barcoding using posterior predictive simulations – Anthony J. Barley – Molecular Ecology

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform – Po-E Li – BioRxiv

GenSeed-HMM: A tool for progressive assembly using profile HMMs as seeds and its application in Alpavirinae viral discovery from metagenomic data – João Marcelo P. Alves – Frontiers in Microbiology

Metabolomics

Human microbial metabolites as a source of new drugs – Somdutta Saha – Drug Discovery Today

More microbiology

Microbiota–mitochondria inter-talk: consequence for microbiota-host interaction – Yann Saint-Georges-Chaumet – Pathogens and Disease

Exploitation by cheaters facilitates the preservation of essential public goods in microbial communities – Clara Moreno-Fenoll – bioRxiv

Accurate and semi-automated analysis of bacterial association with mammalian cells – C.M. Murphy – Journal of Microbiological Methods

Microbes in the news

Fungal DNA, mycotoxins, cat allergens and fatigue in classrooms – Holly Ganz – MicroBEnet

Gum Disease Bacteria Linked to Esophageal Cancer Risk – Newsmax

Video: Virginia Tech scientists turn poo into power – Virginia Tech

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February 17, 2016

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Microbial biomarkers for diabetes, gut sialidases,  pathogens in stranded sea turtles, microbial biodeterioration of an ancient staircase, and how bacterial stay in shape.

Events

‘Microbiome-based Foods for Health and Sustainability’ workshop, 23 February, Brussels – APC Microbiome Institute

Call for Entries! ASM’s 2016 Agar Art Contest. Deadline: May 6.

Human oral microbiome

Intracerebral hemorrhage and deep microbleeds associated with cnm-positive Streptococcus mutans; a hospital cohort study – Shuichi Tonomura – Scientific Reports

Review: Oral Microbiome: Contributions to Local and Systemic Infections – Kerri T. Simpson – Current Oral Health Reports

Human gut microbiome

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes – Moran Yassour – Genome Medicine

Postoperative changes in fecal bacterial communities and fermentation products in obese patients undergoing bilio-intestinal bypass – Vania Patrone – Frontiers in Microbiology

The Effects of Bowel Preparation on Microbiota-Related Metrics Differ in Health and in Inflammatory Bowel Disease and for the Mucosal and Luminal Microbiota Compartments – Rima M Shobar – Clinical and Translational Gastroenterology

Registered report: Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma – John Repass – eLIFE

Review: Sialidases from gut bacteria: a mini-review – Nathalie Juge – Biochemical Society Transactions

Review: Akkermansia muciniphila and its role in regulating host functions – Muriel Derrien – Microbial Pathogenesis

Models of microbiome research

Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice – Jun Li – PNAS

The bacterial microbiome of Dermacentor andersoni ticks influences pathogen susceptibility – Cory A Gall – ISME Journal

Have clay will lay: Chicken: Dietary supplementation with the clay mineral palygorskite affects performance and beneficially modulates caecal microbiota in laying pullets – S. Chalvatzi – Journal of Applied Microbiology

Animal microbiome

Bacterial agents in 248 ticks removed from people from 2002 to 2013 – Camille Aubry – Ticks and Tick-borne Diseases

Bacterial and viral pathogens detected in sea turtles stranded along the coast of Tuscany, Italy – G. Fichi – Veterinary Microbiology

Poor English (but US lab): Identification of Host-Specific Genetic Markers within 16S rDNA Intervening Sequences of 73 Genera of Fecal Bacteria – Zhenyu Shen – Omics’ Journal of Data Mining in Genomics & Proteomics

Editorial: Developmental biology: Females have a lot of guts – Justin Fear – Nature

The sexual identity of adult intestinal stem cells controls organ size and plasticity – Bruno Hudry – Nature

Plant, root, and soil microbiome

Bacterial predator–prey dynamics in microscale patchy landscapes – Felix J. H. Hol – Proceedings of the Royal Society B

Variation in soil microbial communities associated with critically endangered Wollemi pine affects fungal, but not bacterial, assembly within seedling roots – J.L. Rigg – Pedobiologia

The Effects of Nitrogen Fertilizer on Soil Microbial Communities Under Conventional and Conservation Agricultural Managements in a Tropical Clay-Rich Ultisol – Miura, Toshiko – Soil Science

Cover Crop and Irrigation Effects on Soil Microbial Communities and Enzymes in Semiarid Agroecosystems of the Central Great Plains of North America – Francisco J. Calderón – Pedosphere

Effect of soil disinfection with chemical and biological methods on bacterial communities – Md Rokunuzzaman – Egyptian Journal of Basic and Applied Sciences

Water and extremophile microbiome

Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines – Charlotte D. Vavourakis – Frontiers in Microbiology

Characterization of bacterial communities in wetland mesocosms receiving pharmaceutical-enriched wastewater – Dongqing Zhang – Ecological Engineering

Microbial Community Profile and Water Quality in a Protected Area of the Caatinga Biome – Fabyano Alvares Cardoso Lopes – PLOS ONE

Thesis: Tightly-coupled sulfur-cycling microbial mats of the White Point hydrothermal vent field, CA: An analog for deep-sea vents – Priscilla J Miranda – California State University Long Beach

Thesis: The microbial diversity and function of Arctic supraglacial biomes – Stefanie Lutz – University of Leeds

Built environment microbiome

Biodeterioration Risk Threatens the 3100 Year Old Staircase of Hallstatt (Austria): Possible Involvement of Halophilic Microorganisms – Guadalupe Piñar – PLOS ONE

The Black Yeast Exophiala dermatitidis and Other Selected Opportunistic Human Fungal Pathogens Spread from Dishwashers to Kitchens – Jerneja Zupančič – PLOS ONE

Bioinformatics and metagenomics

IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses – Shaman Narayanasamy – BioRxiv

Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads – Yvan Le Bras – GigaScience

Shannon: An Information-Optimal de NovoRNA-Seq Assembler – Sreeram Kannan – BioRxiv

RECKONER: Read Error Corrector Based on KMC – Maciej Długosz – ArXiv

A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing – Tian-Hao Zhang – BMC Genomics

More microbiology

HT: Liz Costello: Universal resilience patterns in complex networks – Jianxi Gao – Nature

Microbially assisted recording of the Earth’s magnetic field in sediment – Xiangyu Zhao – Nature Communications

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection – Jeroen De Smet – The ISME Journal

Discovery of cahuitamycins as biofilm inhibitors derived from a convergent biosynthetic pathway – Sung Ryeol Park – Nature Communications

Review: Staying in Shape: the Impact of Cell Shape on Bacterial Survival in Diverse Environments – Desirée C. Yang – Microbiology and Molecular Biology Reviews

Microbes in the news

Oral bacteria linked to risk of stroke – Betty Coffman – University of Louisville

Opportunistic Fungal Pathogens in Dishwashers and Kitchens – Alex Alexiev – MicroBEnet

UVA: Bacteria Overgrowth Could Be Major Cause of Stunting in Children – University of Virginia Health System – NBC29

A new method to dramatically improve the sequencing of metagenomes – EurekAlert

What your gut bacteria can tell you about type 2 diabetes – MedicalXpress

New anti-biofilm compounds show promise against drug-resistant bacteria linked to hospital infections – Ian Demsky – University of Michigan

Crowdfunding project: How Insects and Bacteria Can Solve Murder Mysteries: estimate the time since death (TSD) at a crime scene – Experiment

Crowdfunding project: E pluribus unum: how honey bee bacteria coordinate behaviors – Irene Newton – Experiment

uBiome Named One of World’s Top 10 Most Innovative Companies in Healthcare by Fast Company – PR Web

MIT Spinout Synlogic Grabs $40M To Program Microbes Into Living Drugs – Luke Timmerman – Forbes

Science, publishing, and career

Biologists urged to hug a preprint: ASAPbio meeting discusses the ins and outs of posting work online before peer review – Ewen Callaway – Nature

Accelerating Science with Preprints – Peter Binfield – PeerJ Blog

XY Bias: How Male Biology Students See Their Female Peers. In three large classes, men overrated the abilities of male students above equally talented and outspoken women – Ed Yong – The Atlantic

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February 11, 2016

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Sulphate reducing bacteria impair memory in mice, gastric microbiota after partial gastrectomy, geomicrobiology of the earth’s deep subsurface, and a viral genome assembly pipeline.

Events

Third International Workshop on Biological Soil Crusts, September 26-30, 2016 – Moab, Utah, USA

Human gut microbiota

Gastric microbiota and predicted gene functions are altered after subtotal gastrectomy in patients with gastric cancer – Ching-Hung Tseng – Scientific Reports

Research highlight: Gut microbiota: Microbes offer engineering strategies to combat cancer – Susan E. Erdman – Nature Reviews Gastroenterology & Hepatology

Review: The Reciprocal Interactions between Polyphenols and Gut Microbiota and Effects on Bioaccessibility – Tugba Ozdal – MDPI Nutrients

Review: Learning from microbial strategies for polysaccharide degradation – Glyn R. Hemsworth – Biochemical Society Transactions

Book chapter: Interactions Between Wine Polyphenols and Gut Microbiota – Carolina Cueva – Wine Safety, Consumer Preference, and Human Health

Microbiome models

Mice: Sulfate-reducing bacteria impairs working memory in mice – Nathaniel L. Ritz – Physiology & Behavior

Rats: Whole Rye Consumption Improves Blood and Liver n-3 Fatty Acid Profile and Gut Microbiota Composition in Rats – Fayçal Ounnas – PLOS ONE

Animal microbiome

Nematodes: Microbial communities in Globodera pallida females raised in potato monoculture soil – Caroline Eberlein – Phytopathology

Sponges: Distinctive features of the microbial diversity and the polyketide synthase genes spectrum in the community of the endemic Baikal sponge Swartschewskia papyracea – O. V. Kaluzhnaya – Russian Journal of Genetics

Plant, root, and soil microbiome

Medicago truncatula Gaertn. as a model for understanding the mechanism of growth promotion by bacteria from rhizosphere and nodules of alfalfa – Anna Kisiel – Planta

Relationship between in vitro characterization and comparative efficacy of plant growth-promoting rhizobacteria for improving cucumber salt tolerance – Sajid Mahmood Nadeem – Archives of Microbiology

Geomicrobiology and Metagenomics of Terrestrial Deep Subsurface Microbiomes –
M. Itävaara – Advances in Applied Microbiology

Soil Nitrogen Status Modifies Rice Root Response to Nematode-Bacteria Interactions in the Rhizosphere – Yanhong Cheng – PLOS ONE

Water microbiome

Pollution-induced community tolerance for in situ assessment of recovery in river microbial communities following the ban of the herbicide diuron – Stéphane Pesce – Agriculture, Ecosystems & Environment

Built environment microbiology

Characterization of a drinking water distribution pipeline terminally colonized by Naegleria fowleri – Matthew J. Morgan – Environmental Science & Technology

Mitigation of biofilm formation on corrugated cardboard fresh produce packaging surfaces using a novel thiazolidinedione derivative integrated in acrylic emulsion polymers – Michael Brandwein – Frontiers in Microbiology

Bioreactor microbiology

Anaerobic digestion of biowaste under extreme ammonia concentration: Identification of key microbial phylotypes – Simon Poirier – Bioresource Technology

Bioinformatics, viruses, metabolomics, and metagenomics

VirusTAP: Viral Genome-Targeted Assembly Pipeline – Akifumi Yamashita – Frontiers in Microbiology

The secondary metabolite bioinformatics portal: Computational tools to facilitate synthetic biology of secondary metabolite production – Tilmann Weber – Synthetic and Systems Biotechnology

Microbes in the news

Inhibiting age-related inflammation maintains healthy gut microbiota and extends lifespan – MedicalXpress

An Occupy Movement for the Symbiome – Marti Davidson Sichel – GenEngNews

Middletown High students make bacteria glow in mobile lab – Sylvia Carignan – Frederick News Post
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Electric-car battery materials could harm key soil bacteria – American Chemical Society

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February 10, 2016

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Socioeconomic status and microbiota diversity, metagenome of a carnivorous plant, microbiota of homes of CF patients, and high-resolution phylogenetic microbial community profiling.

Events

ASM Microbe 2016, June 16-20, Boston MA. With opening keynote lecture by Bill Gates

SC2: Microbiome: Sorting out the hype from the hope – March 6-11 2016, San Francisco

Probiotics and Prebiotics – June 21-23, Budapest

Pregnancy and birth

Routine Use of Probiotics in Preterm Infants: Longitudinal Impact on the Microbiome and Metabolome – Abdulkadir B. – Neonatology

Human oral microbiome

Isolation of Propionibacterium acnes among the microbiota of primary endodontic infections with and without intraoral communication – Sadia Ambreen Niazi – Clinical Oral Investigations

Human gut microbiome

Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach – Francesca Turroni – The ISME Journal

Lower Neighborhood Socioeconomic Status Associated with Reduced Diversity of the Colonic Microbiota in Healthy Adults – Gregory E. Miller – PLOS ONE

The features of mucosa-associated microbiota in primary sclerosing cholangitis –
J. Torres – Alimentary Pharmacology & Therapeutics

Review: Physiological Role of Gut Microbiota for Maintaining Human Health – Andoh A. – Digestion

Editorial: You Are What You Feed Your Gut Microbiome – Joseph E. Scherger – Health Affairs

Review: Gastroenvironmental distress: metaphorical antecedents of the gut microbiome – Nitin K Ahuja – Medical Humanities

Review: Fostering of advanced mutualism with gut microbiota by Immunoglobulin A – Duncan B. Sutherland – Immunological Reviews

Models of microbiome research

Drosophila: Preventing Age-Related Decline of Gut Compartmentalization Limits Microbiota Dysbiosis and Extends Lifespan – Hongjie Li – Cell Host & Microbe

Editorial: Microbes without Borders: Decompartmentalization of the Aging Gut – Erin S. Keebaugh – Cell Host & Microbe

Mice (and humans): Intestinal REG3 Lectins Protect against Alcoholic Steatohepatitis by Reducing Mucosa-Associated Microbiota and Preventing Bacterial Translocation – Lirui Wang – Cell Host & Microbe

Editorial: Alcohol Lowers Your (Intestinal) Inhibitions – Namrata Iyer – Cell Host & Microbe

Mice: Daikenchuto (TU-100) shapes gut microbiota architecture and increases the production of ginsenoside metabolite compound K – Takumu Hasebe – Pharmacology Research & Perspectives

Editorial: Microbiota Control of Malaria Transmission – Miguel P. Soares – Trends in Parasitology

Animal microbiome

Beetles: Trophic and Non-Trophic Interactions in a Biodiversity Experiment Assessed by Next-Generation Sequencing – Julia Tiede – PLOS ONE

Plant, root, and soil microbiome

The Metagenome of Utricularia gibba’s Traps: Into the Microbial Input to a Carnivorous Plant – Luis David Alcaraz – PLOS ONE

Enhancement of drought stress tolerance in crops by plant growth promoting rhizobacteria – Sai Shiva Krishna Prasad Vurukonda – Microbiological Research

Actinobacteria from Arid and Desert Habitats: Diversity and Biological Activity –
Fatemeh Mohammadipanah – Frontiers in Microbiology

Organic Fertilization in Traditional Mediterranean Grapevine Orchards Mediates Changes in Soil Microbial Community Structure and Enhances Soil Fertility – Fuensanta García-Orenes – Land Degradation & Development

Effects of plant functional group loss on soil biota and net ecosystem exchange: a plant removal experiment in the Mongolian grassland – Dima Chen – Journal of Ecology

Water microbiome

Plankton networks driving carbon export in the oligotrophic ocean – Lionel Guidi – Nature

Built environment microbiome

Assessment of the Microbial Constituents of the Home Environment of Individuals with Cystic Fibrosis (CF) and Their Association with Lower Airways Infections – Alya Heirali – PLOS ONE

Metabolomics

Microbial metabolomics in open microscale platforms – Layla J. Barkal – Nature Communications

More microbiology

Open for discussion: Bacterial sequences detected in 99 out of 99 serum samples from Ebola patients – Marina Manrique – bioRxiv

Ethanol Production by Selected Intestinal Microorganisms and Lactic Acid Bacteria Growing under Different Nutritional Conditions – Fouad M. F. Elshaghabee – Frontiers in Microbiology

Rapid radiation in bacteria leads to a division of labour – Wook Kim – Nature Communications

Total biosynthesis of opiates by stepwise fermentation using engineered Escherichia coli – Akira Nakagawa – Nature Communications

Bioinformatics and metagenomics

PhyloTags: High-resolution phylogenetic microbial community profiling – Esther Singer – The ISME Journal

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum – Karthik Anantharaman – PeerJ

Microbes in the news

The Good, the Bad and the Microbiome – Rachel Reisig – University of Minnesota

Unraveling the Mysterious Function of the Microbiome – by Mike Orcutt – MIT Technology Review

Wound-healing intestinal bacteria: Like shrubs after a forest fire
Akkermansia + other anaerobic bacteria temporarily bloom – EurekAlert

San Diego Scientists Find Data Brewing In Local Fermentation Culture – David Wagner – KPBS

Bacteria Have Ability to ‘See,’ Eye-Opening Study Finds – Maggie Fox – NBC News

A gut feeling about bacteria: Men are from Mars, women are from Venus – and their gut bacteria is just as different. – The Senior

How Your Gut Affects Your Bones. The surprising new science of how intestinal bacteria control bone strength – Rana Samadfam – Scientific American

Scientists Discover New Bacteria Responsible For Lyme Disease – David Beasly – Huffington Post

Overhyped: Sci-Q: The Science Of Love: The role of the microbiome in romantic attraction

Science, publishing, and career

Improving the peer-review process and editorial quality: key errors escaping the review and editorial process in top scientific journals – Antoni Margalida – PeerJ

Does it take too long to publish research? – Kendall Powell – Nature

The history of publishing delays – Daniel Himmelstein

The sexual misconduct case that has rocked anthropology – Michael Balter – Science
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February 9, 2016

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Human skin metagenome, gout patients, malaria and gut microbes, the secrets of the rhizosphere, and single-stranded DNA phages.

Events

2nd Annual Translational Microbiome Conference – April 20-21 2016, Boston MA

Pregnancy and birth

Longitudinal Prediction of the Infant Gut Microbiome with Dynamic Bayesian Networks – Michael J. McGeachie – Scientific Reports

Review: Gut microbiota and the pathogenesis of necrotizing enterocolitis in preterm neonates – Nadim Cassir – Future Microbiology

Human skin microbiome

Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing – Yu-Chih Tsai – mBio

Human urinary tract microbiome

Male non-gonococcal urethritis: From microbiological etiologies to demographic and clinical features – Shin Ito – International Journal of Urology

Research highlight: Altered gut microbiota in CKD – Jessica K. Edwards – Nature Reviews Nephrology

Human respiratory microbiome

Review: Microbiome, biofilms, and pneumonia in the ICU – Massimiliano Pirrone – Current Opinion in Infectious Diseases

Human gut microbiome

Intestinal Microbiota Distinguish Gout Patients from Healthy Humans – Zhuang Guo – Scientific Reports

Effect of Proton Pump Inhibitors and Antibiotics on the Gut Microbiome of Hospitalised Older Persons – Caoilfhionn O’Donoghue – Journal of Infection

Editorial: A metabolic bridge between microbiota and humans – Kiyoshi Takeda – Nature Reviews Immunology

Review: The Gut Microbiome: Potential Innovations for the Understanding and Treatment of Psychopathology – Matilda E. Nowakowski – Canadian Psychology/Psychologie canadienne

Review: Metabolic modeling with big data and the gut microbiome – Jaeyun Sung – Applied & Translational Genomics

Review: The influence of commensal bacteria on infection with enteric viruses – Stephanie M. Karst – Nature Reviews Microbiology

Review: One more role for the gut: microbiota and blood brain barrier – Laure Michel – Annals of Translational Medicine

Review: Expanding role of gut microbiota in lipid metabolism – Anatole Ghazalpour – Current Opinion in Lipidology

Models of microbiome research

Mice: Composition of the gut microbiota modulates the severity of malaria – Nicolas F. Villarino – PNAS

Mice: Lambda Interferon Restructures the Nasal Microbiome and Increases Susceptibility to Staphylococcus aureus Superinfection – Paul J. Planet – mBio

Dogs: Longitudinal evaluation of the skin microbiome and association with microenvironment and treatment in canine atopic dermatitis – Charles W. Bradley – Journal of Investigative Dermatology

Goats: The effect of helminth infection on the microbial composition and structure of the caprine abomasal microbiome – Robert W. Li – Scientific Reports

More goats: Grain-rich diets altered the colonic fermentation and mucosa-associated bacterial communities and induced mucosal injuries in goats – Huimin Ye – Scientific Reports

Rats: The Colonic Microbiome and Epithelial Transcriptome Are Altered in Rats Fed a High-Protein Diet Compared with a Normal-Protein Diet – Chunlong Mu – The Journal of Nutrition

Rats: Resistant Starch Alters Gut Microbiome and Metabolomics Profiles Concurrent with Amelioration of Chronic Kidney Disease in Rats – Dorothy A. Kieffer – American Journal of Physiology – Renal Physiology
http://ajprenal.physiology.org/content/early/2016/02/01/ajprenal.00513.2015.abstract

Drosophila: From pathogens to microbiota: how Drosophila intestinal stem cells react to gut microbes – Alessandro Bonfini – Developmental & Comparative Immunology

Animal microbiome

Host plant determines the population size of an obligate symbiont Buchnera aphidicola in aphids – Yuan-Chen Zhang – Applied and Environmental Microbiology

Altered Carbohydrates Allocation by Associated Bacteria-fungi Interactions in a Bark Beetle-microbe Symbiosis – Fangyuan Zhou – Scientific Reports

Plant, root, and soil microbiome

Soil amendments yield persisting effects on the microbial communities—a 7-year study – Catherine L. Reardon – Applied Soil Ecology

Microbial genetic and enzymatic responses to an anthropogenic phosphorus gradient within a subtropical peatland – Elise Morrison – Geoderma

Salinity altered root distribution and increased diversity of bacterial communities in the rhizosphere soil of Jerusalem artichoke – Hui Yan – Scientific Reports

Development of oligonucleotide microarrays for simultaneous multi-species identification of Phellinus tree-pathogenic fungi – Yuh Tzean – Microbial Biotechnology

Dilution reveals how viral lysis and grazing shape microbial communities – Jacob A. Cram – Limnology and Oceanography

Response of Soil Bacterial Community Structure to Land-use Conversion of Natural Forests in Maoershan National Forest Park, China – Fanjuan Meng – Molecular Soil Biology

Editorial: Unlocking the Secrets of the Rhizosphere – Susanne C. Brink – Trends in Plant Science

Spotlight: The soil-borne supremacy – Corné M.J. Pieterse – Trends in Plant Science

Water and pollution microbiome

Temporal and spatial changes of microbial community in an industrial effluent receiving area in Hangzhou Bay – Yan Zhang – Journal of Environmental Sciences

Built environment microbiome

Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite – Dongshan An – Frontiers in Microbiology

Viruses and phages

Viral metagenomics: are we missing the giants? – S Halary – Current Opinion in Microbiology

Single-Stranded DNA Phages: From Early Molecular Biology Tools to Recent Revolutions in Environmental Microbiology – Anna J. Székely – FEMS Microbiology Letters

Sequencing techniques

A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms – Nagaraju Indugu – PeerJ

Bioinformatics and metagenomics

Improved environmental genomes via integration of metagenomic and single-cell assemblies – Daniel R. Mende – Frontiers in Microbiology

PhyloPythiaS+: a self-training method for the rapid reconstruction of low-ranking taxonomic bins from metagenomes – Ivan Gregor- PeerJ

Estimating and comparing microbial diversity in the presence of sequencing errors – Chun-Huo Chiu – PeerJ

Metabolomics

Metabolic modeling with big data and the gut microbiome – Jaeyun Sung – Applied & Translational Genomics

More microbiology

Cyanobacteria use micro-optics to sense light direction – Nils Schuergers – eLIFE

Ultrasensitive Detection of Bacteria by Targeting Abundant Transcripts – Xinhui Wang – Scientific Reports

Microbes in the news

Pill measures gut gas – Swallowable tool may eventually help reveal digestive problems – Sarah Schwartz – Science News

Gut environment could reduce severity of malaria – EurekAlert

Great stockphoto: Hibernation Helpers: Gut microbes may help regulate the metabolic changes a bear experiences before and during hibernation, scientists show – Catherine Offord – The Scientist

The complex marketing of “probiotic” cosmetics – Éva Lagarde – Premium Beauty News

Plants trick bacteria into attacking too soon – Chris Samoray – Science News

Obstructive sleep apnea-induced hypertension linked to gut microbiome – Baylor College of Medicine

Includes Rob Knight. HT: Tomer Altman. Deepak Chopra Convenes 30+ of the World’s Preeminent Thought Leaders, Philosophers, Scientists, Musicians and Artists to Explore Consciousness at a 3-Day Symposium This Fall – PR Newswire

Researchers identify most dangerous strains of often-deadly bacteria – University of Maryland – EurekAlert

Science, publishing, and career

Harvard Medical School students decry lack of diversity – Melissa Baily – STATnews

I make an appearance here: Getting credit for peer review – Sandeep Ravindran – Science

Change the system to halt harassment – Joan Schmelz – Nature

Bik’s Picks

The peptidergic control circuit for sighing – Peng Li – Nature

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February 6, 2016

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Your Saturday morning Microbiome Digest.

Jobs and events

Postdoctoral Associate, Chicago, Illinois – Shedd Aquarium Microbiome Project

Human urinary tract microbiome

The Bladder Is Not Sterile: History and Current Discoveries on the Urinary Microbiome – Krystal Thomas-White – Current Bladder Dysfunction Reports

Human gut microbiome

American Gut: Researchers Launch Open-Access Gut Project – Nancy Averett – BioScience

Animal microbiome

Faecal virome of red foxes from peri-urban areas – Ivana Lojkić – Comparative Immunology, Microbiology and Infectious Diseases

Closely coupled evolutionary history of ecto- and endosymbionts from two distantly-related animal phyla – Judith Zimmermann – Molecular Ecology

Plant, root, and soil microbiome

Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression – Menno van der Voort – Ecology Letters

Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA – Lucie Zinger – Soil Biology and Biochemistry

Water and extremophile microbiome

Metagenomic Analysis Reveals Symbiotic Relationship among Bacteria in Microcystis-Dominated Community – Meili Xie – Frontiers in Microbiology

Metagenomic Analysis of Virioplankton of the Subtropical Jiulong River Estuary, China – Lanlan Cai – MDPI Viruses

Hydrocarbon pollutants shape bacterial community assembly of harbor sediments – Marta Barbato – Marine Pollution Bulletin

Thesis: The Impact of Temperature, pH and Environmental Heterogeneity on Prokaryotic
Diversity in Yellowstone National Park Thermal Springs – Xiaoben Jiang – The University of New Mexico

Drinking water and waste microbiome

Archaeal community in a human-disturbed watershed in southeast China: diversity, distribution, and responses to environmental changes – Anyi Hu – Applied Microbiology and Biotechnology

Comparison of Particle-Associated Bacteria from a Drinking Water Treatment Plant and Distribution Reservoirs with Different Water Sources – G. Liu – Scientific Reports

Biostimulation of metal-resistant microbial consortium to remove zinc from contaminated environments – Isis E. Mejias Carpio – Science of the Total Environment

Review: Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges – Emmanuelle I. Prest – Frontiers in Microbiology

Built environment microbiome / microbes in space

Growth of 48 built environment bacterial isolates on board the International Space Station (ISS) – David A Coil – PeerJ

The Last Possible Outposts for Life on Mars – Davila Alfonso F. – Astrobiology

Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy – Stefano Campanaro – Biotechnology for Biofuels

Bioinformatics and metagenomics

TruSPAdes: barcode assembly of TruSeq synthetic long reads – Anton Bankevich – Nature Methods

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies – Tom O. Delmont – PeerJ

Thesis: A Case Study Tested Framework for Multivariate Analyses of Microbiomes: Software for Microbial Community Comparisons – Eric M. Spaulding – University of Montana – Missoula
Metabolomics

Twin metabolomics: The key to unlocking complex phenotypes in nutrition research – Rebecca Barron – Nutrition Research

Increasing metagenomic resolution of microbiome interactions through functional phylogenomics and bacterial sub-communities – Angélica Cibrián-Jaramillo – Frontiers in Genetics

Microbes in the news

Buffalo Wild Wings Hit By Norovirus Investigation Before Super Bowl Binge – Venessa Wong – BuzzFeed

Explainer: what is the gut microbiota and how does it affect mind and body? – Senaka Ranadheera – The Conversation

Not all statements are true: Microbial miracle workers – Jay Keche – Indiana Daily Student

Science, publishing, and career

Gaming Metrics conference (Feb 4-5, UC Davis) about science misconduct, fake journals, and citation games – Storify Day 1 by Jonathan Eisen
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January 27, 2016 – second edition

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A call from the White House, synergy between Mycoplasma and Gardnerella, urinary microbiome, sarcoidosis, and a hiking guide to microbes on the seafloor.

Events

The White House wants feedback from “All Microbiome-Science Champions” – give it – give it now – Jonathan Eisen – MicroBEnet
and
Calling All Microbiome-Science Champions! – Jo Handelsman and Elizabeth Stulberg – The White House

General human microbiome

Review: Exploring and Understanding the Biochemical Diversity of the Human Microbiota – Nitzan Koppel – Cell Chemical Biology

Pregnancy and birth

The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content – Zachery T. Lewis – PeerJ

The common vaginal commensal bacterium Ureaplasma parvum is associated with chorioamnionitis in extreme preterm labour – Ciara Cox – The Journal of Maternal-Fetal & Neonatal Medicine

Human vaginal microbiome

Mycoplasma hominis and Gardnerella vaginalis display a significant synergistic relationship in bacterial vaginosis – C. Cox – European Journal of Clinical Microbiology & Infectious Diseases
Human oral microbiome

The yield and quality of cellular and bacterial DNA extracts from human oral rinse samples are variably affected by the cell lysis methodology – Mohsen Sohrabi – Journal of Microbiological Methods

Human skin microbiome

Note: 1 person per study group: Skin microbiota of first cousins affected by psoriasis and atopic dermatitis – Lorenzo Drago – Clinical and Molecular Allergy

Human urinary tract microbiome

Review: The human urinary microbiome and how it relates to urogynecology – Jenifer Schneeweiss – International Urogynecology Journal

Human gut microbiome

Metabolomics connects aberrant bioenergetic, transmethylation, and gut microbiota in sarcoidosis – Andreea Geamanu – Metabolomics

Review: Role of antibiotics for treatment of inflammatory bowel disease – Orna Nitzan – World Journal of Gastroenterology

Review: Gut microbiota imbalance and colorectal cancer – Johan Gagnière – World Journal of Gastroenterology

Animal models

In mice: A detrimental role of immunosuppressive drug, dexamethasone, during Clostridium difficile infection in association with a gastrointestinal microbial shift – Hyeun Bum Kim – Journal of Microbiology and Biotechnology

Animal microbiome

Diversity of the gastric microbiota in Thoroughbred racehorses having gastric ulcer – Hee-Jin Dong – Journal of Microbiology and Biotechnology

Plant, root, and soil microbiome

Long term repeated fire disturbance alters soil bacterial diversity but not the abundance in an Australian wet sclerophyll forest – Ju-pei Shen – Scientific Reports

Bacterial Diversity and Community Structure in Two Bornean Nepenthes Species with Differences in Nitrogen Acquisition Strategies – Wiebke Sickel – Microbial Ecology

Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia – Yuji Jiang – Soil Biology and Biochemistry

Emergence in mapping microbial diversity in tea (Camellia sinensis (L.) O. Kuntze) soil of Assam, North-East India: A novel approach – PN Bhattacharyya – European Journal of Biotechnology and Bioscience

High-Throughput Sequencing Analysis of the Endophytic Bacterial Diversity and Dynamics in Roots of the Halophyte Salicornia europaea – Shuai Zhao – Current Microbiology

Water and waste microbiome

Use of matrix-assisted laser desorption/ionization–time of flight (MALDI–TOF) mass spectrometry for bacterial monitoring in routine analysis at a drinking water treatment plant – Laura Sala-Comorera – International Journal of Hygiene and Environmental Health

Extremophile microbiome

The Guaymas Basin hiking guide to hydrothermal mounds, chimneys and microbial mats: complex seafloor expressions of subsurface hydrothermal circulation – Andreas Teske – Frontiers in Microbiology

Bioinformatics and metagenomics

Bayesian Nonparametric Ordination for the Analysis of Microbial Communities – Boyu Ren – ArXiv

Keemei: cloud-based validation of tabular bioinformatics file formats in Google Sheets – Jai Ram Rideout – PeerJ Preprint

Characterization of sequence-specific errors in various next-generation sequencing systems – Sunguk Shin – Molecular Biosystems

Stochastic neutral modelling of the Gut Microbiota’s relative species abundance from next generation sequencing data – Claudia Sala – BMC Bioinformatics

Protocol: “Deciphering Archaeal Communities” Omics Tools in the Study of Archaeal Communities – Lejla Pašić – Microbial Environmental Genomics (MEG)

Protocol: Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches – Anne Schöler – Microbial Environmental Genomics (MEG)

Science, publishing, and career

Funding: What stops women getting more grants? – David McAllister – Nature

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