Category Archives: Water microbiome

February 20, 2016

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Effects of ocean acidification, structural proteins in viral dark matter, and microbiome art. Also check out my new post at MicroBE.net with new papers on microbiome of the built environment.

Human respiratory tract microbiome

Review: How Recent Advances in Molecular Tests Could Impact the Diagnosis of Pneumonia – David Murdoch – Expert Review of Molecular Diagnostics

Microbiome models

In vitro fermentation of alginate and its derivatives by human gut microbiota – Miaomiao Li – Anaerobe

Plant, root, and soil microbiome

Changes of soil prokaryotic communities after clear cutting in a karst forest: evidences for cutting-based disturbance promoting deterministic processes – Xiao Zhang – FEMS Microbiology Ecology

Use of mulberry–soybean intercropping in salt–alkali soil impacts the diversity of the soil bacterial community – Xin Li – Microbial Biotechnology

Distinct Habitats Select Particular Bacterial Communities in Mangrove Sediments – Lidianne L. Rocha – International Journal of Microbiology

Water and ice microbiome

Quantification of the effects of ocean acidification on sediment microbial communities in the environment: the importance of ecosystem approaches – Christiane Hassenrück – FEMS Microbiology Ecology

Bacterial communities from Arctic seasonal sea ice are more compositionally variable than those from multi-year sea ice – Ido Hatam – The ISME Journal

Bioreactor and waste microbiology

Biodegradation of different petroleum hydrocarbons by free and immobilized microbial consortia – Tiantian Shen – Environmental Science: Processes & Impacts

Bioinformatics and metagenomics

Recent Developments in Using Advanced Sequencing Technologies for the Genomic Studies of Lignin and Cellulose Degrading Microorganisms – Ayyappa kumar Sista Kameshwar – International Journal of Biological Sciences

DUDE-Seq: Fast, flexible, and robust denoising of nucleotide sequences – Byunghan Lee – Bioinformatics

HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing – Ramin Karimi – Evolutionary Bioinformatics

FLDS: A Comprehensive dsRNA Sequencing Method for Intracellular RNA Virus Surveillance – Syun-ichi Urayama – Microbes and Environments

Based on my old discovery of the mycobacterial CRISPR: SpoTyping: fast and accurate in silico Mycobacterium spoligotyping from sequence reads – Eryu Xia – Genome Medicine

Microbial ecology

A tradeoff between the ecological and evolutionary stabilities of public goods genes in microbial populations – Joseph Rauch – BioRxiv

Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations – Tatiana Shashkova – PLOS ONE

Proteomics

Illuminating structural proteins in viral “dark matter” with metaproteomics – Jennifer R. Brum – PNAS

Microbes in the news

‘Unhealthy’ Microbiomes Could Promote Metabolic Disease. UCSF Symposium Explores Vulnerability and Malleability of Microbes in Human Gut – Nicholas Weiler – University of California San Francisco

Unusual sugar in leafy greens may help gut bacteria protect health – Catharine Paddock – Medical News Today

One startup’s plan to grow more crops: put the germs back in. Indigo claims it can dramatically boost yields by restoring plant’s microbiome – Ben Popper – The Verge

The intestinal microbiota—a new ally for optimum growth – Medical Xpress

Bacteria In Contact Lenses May Cause Inflammatory Response Leading To Microbial Keratitis / Gross Science Video with Anna Rothschild – Lizette Borreli – Medical Daily

Bacteria Hysteria

Tea crawling with harmful bacteria and food trays covered in faeces: The horror health threats facing airline passengers – The Sun

Microbes and art

Faces of BioArt: Sonja Bäumel’s Microbiome Portraits and Bacterial Clothing – Labiotech

Science, publishing, and career

Put the “Ph” Back in PhD. We need big thinkers, but the current system teaches students to think small – Arturo Casadevall

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February 18, 2016

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Two papers from the Gordon lab today about malnutrition and gut microbes, connecting gut microbes with host chitin, fur seals, and analyzing soil communities for forensic use.

Pregnancy and birth

(partly in mice) Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children – Laura V. Blanton – Science

Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition – Mark R. Charbonneau – Cell

Editorial: The right gut microbes help infants grow – Elizabeth Pennisi – Science

Stool bacterial load in preterm infants with necrotising enterocolitis – Bashir Abdulkadir – Early Human Development

Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study – Guilherme Calvet – The Lancet Infectious Diseases

Human gut microbiome

Gut Microbiota Predict Pulmonary Infiltrates After Allogeneic Hematopoietic Cell Transplantation – Bianca Harris – Am J Respir Crit Care Med

Members of the Intestinal Microbiota Are Associated with Relapse after Allogeneic Hematopoietic Stem Cell Transplantation – Jonathan U. Peled – Biology of Blood and Marrow Transplantation

Conference abstract: Fecal Microbiota Transplant Is a Potentially Safe and Effective Treatment for Clostridium Difficile Infection in Hematopoietic Stem Cell Recipients – Shannon Falconer – Biology of Blood and Marrow Transplantation

The impact of gut colonization by antibiotic-resistant bacteria on the outcomes of allogeneic hematopoietic stem-cell transplantation: a retrospective, single-center study – Jaroslaw Bilinski – Biology of Blood and Marrow Transplantation

 

PhD Thesis: Temporal Modulation of Gut Microbiome and Metabolome by Morphine – Fuyuan Wang – University of Minnesota

Research highlight: Frailty associated with gut microbiota – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Review: Exploring the Microbiome in Heart Failure – Takeshi Kitai – Current Heart Failure Reports

Perspective: The microbiome and development of allergic disease – Susan V. Lynch – Current Opinion in Allergy and Clinical Immunology

Hypothesis: The gut microbiota: A puppet master in the pathogenesis of endometriosis? – Matthias W. Laschke – American Journal of Obstetrics and Gynecology

Editorial: Microbiota, Obesity and Malnutrition – Didier Raoult – Microbial Pathogenesis

Review: Protective and Pro-Inflammatory Roles of Intestinal Bacteria – Cynthia Reinoso Webb – Pathophysiology

Models of microbiome

Mice: Hepatic circadian clock oscillators and nuclear receptors integrate microbiome-derived signals – Alexandra Montagner – Scientific Reports

Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition – Martin Schwarzer – Science

Mice: Butyrate production from high-fiber diet protects against lymphoma tumor – Wei Wei – Leukemia & Lymphoma

Drosophila: Sex difference in pathology of the ageing gut mediates the greater response of female lifespan to dietary restriction – Jennifer C Regan – eLIFE

Mice: Treatment with a Monoclonal Anti-IL-12p40 Antibody Induces Substantial Gut Microbiota Changes in an Experimental Colitis Model – Josué Castro-Mejía – Gastroenterology Research and Practice

Mice: Diets enriched with cranberry beans alter the microbiota and mitigate colitis severity and associated inflammation – Jennifer M. Monk – The Journal of Nutritional Biochemistry

Research Highlight: Microbiota promote gut healing – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Gut immunity in a protochordate involves a secreted immunoglobulin-type mediator binding host chitin and bacteria – Larry J. Dishaw – Nature Communications

Characterisation of the faecal bacterial community of wild young South American (Arctocephalus australis) and Subantarctic fur seals (Arctocephalus tropicalis) – Aline Weber Medeiros – FEMS Microbiology Ecology

16S rRNA amplicon sequencing for epidemiological surveys of bacteria in wildlife: the importance of cleaning post-sequencing data before estimating positivity, prevalence and co-infection – Maxime Galan – bioRxiv

Nestedness of hoopoes’ bacterial communities: symbionts from the uropygial gland to the eggshell – Juan J. Soler – Biological Journal of the Linnean Society

Plant, root, and soil microbiome

Biogeographic Patterns Between Bacterial Phyllosphere Communities of the Southern Magnolia (Magnolia grandiflora) in a Small Forest – Bram W. G. Stone – Microbial Ecology

Culturable endophytic bacteria from the salt marsh plant Halimione portulacoides: phylogenetic diversity, functional characterization, and influence of metal(loid) contamination – Cátia Fidalgo – Environmental Science and Pollution Research

Next-Generation Sequencing of the Bacterial 16S rRNA Gene for Forensic Soil Comparison: A Feasibility Study – Ellen M. Jesmok – Journal of Forensic Sciences

Water microbiome

Sediments and Soils Act as Reservoirs for Taxonomic and Functional Bacterial Diversity in the Upper Mississippi River – Christopher Staley – Microbial Ecology

The Influence of Time and Plant Species on the Composition of the Decomposing Bacterial Community in a Stream Ecosystem – Adam S. Wymore – Microbial Ecology

Built environment microbiome

Commentary: Making microbiology of the built environment relevant to design – G. Z. Brown – Microbiome

Food microbiology

Changes of microbial spoilage, lipid-protein oxidation and physicochemical properties during post mortem refrigerated storage of goat meat – Azad Behnan Sabow – Animal Science Journal

Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota – Alejandra Escobar-Zepeda – Food Microbiology

Bioinformatics

An analysis of human microbe–disease associations – Wei Ma – Briefings in Bioinformatics

FN-Identify: Novel Restriction Enzymes-Based Method for Bacterial Identification in Absence of Genome Sequencing – Mohamed Awad – Advances in Bioinformatics

Microbial ecology

Capturing the Dynamic, Heterogeneous Response of Microbes to their Environment in the Human Microbiome – Julie Biteen – Biophysical Journal

Perspective: Microbial community modeling using reliability theory – Julie L Zilles – The ISME Journal

Microbes in the news

Could the right gut microbes help fight childhood malnutrition? – Rachel Feltman – Washington Post

Breast Milk Sugars Support Infant Gut Health – Anna Azvolinsky – The Scientist

Targeting gut microbes may reverse effects of childhood malnutrition
Healthy microbes, breast milk component suggest new treatment approach, mouse study shows – Julie Evangelou Strait – Washington University

How Microbes Make Malnutrition Worse. And how they can be marshaled to fight it – Ed Yong – The Atlantic

 

The Mushroom Death Suit is the latest in post-mortem, eco-friendly fashion – Atlas Obscura

Through Metagenomics Analysis, Researchers Uncover Zika Virus Genome in Amniotic Fluid – Genome Web

What’s bugging you now? The amazing potential of our bodies’ own bacteria – Trisha Macnair – Spectator Health

Gut bacteria may be the difference between well-fed and malnourished – Jacob Kastrenakes – The Verge

Creative Minds: Bacteria, Gene Swaps, and Human Cancer, featuring Julie Dunning Hotopp – Francis Collins – NIH Director’s Blog

This Startup Wants to Use Bacteria to Revolutionize How Our Food Is Produced – Beth Kowitt – Fortune

Bacteria Hysteria

Dad warns parents about Sistema Twist ‘N’ Sip drink bottles ‘hoarding bacteria’ – Stuff

Breast Milk Bought Online May Contain Bacteria That Could Harm Your Child, Investigation Finds – Inside Edition

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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 16, 2016

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Today we’ll go to the extremes: Life in hydrogen sulfide rich environments, subsurface Archaea, subseafloor Fungi, and pit latrines.

Events

NIOO Summer course: identifying terrestrial and freshwater nematodes – June 13-24, Wageningen, The Netherlands

Human respiratory microbiome

Concealed Carry: Hidden Staphylococcus aureus Carriage: Overrated or Underappreciated? – Alex van Belkum – mBio

Human gut microbiome

Review: Imbalance of Gastrointestinal Microbiota in the Pathogenesis of Helicobacter pylori-Associated Diseases – Cong He – Helicobacter

Editorial: We are not alone: Understanding the Contributions of Intestinal Microbial Communities and the Congested Gut in Heart Failure – WH Wilson Tang – JACC Heart Failure

Research Highlight: Microbiota predicts side-effects of immunotherapy – Yvonne Bordon – Nature Reviews Microbiology

Models of microbiome research

Rats: Effects of neutrophils peptide-1 transgenic Chlorella ellipsoidea on the gut microbiota of male Sprague–Dawley rats, as revealed by high-throughput 16S rRNA sequencing – Mingzhang Guo – World Journal of Microbiology and Biotechnology

Fish: Correlation between microbiota and growth in Mangrove Killifish (Kryptolebias marmoratus) and Atlantic cod (Gadus morhua) – Torunn Forberg – Scientific Reports

Rats: Diet-induced changes in maternal gut microbiota and metabolomic profiles influence programming of offspring obesity risk in rats – Heather A. Paul – Scientific Reports

Plant, root, and soil microbiome

Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development –
Eline H. Verbon – Trends in Plant Science

Water and extremophile microbiome

Mechanisms underlying adaptation to life in hydrogen sulfide rich environments – Joanna L. Kelley – Molecular Biology and Evolution

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces – William Orsi – PLOS ONE

Succession of lignocellulolytic bacterial consortia bred anaerobically from lake sediment – Elisa Korenblum – Microbial Biotechnology

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea – Brett J. Baker – Nature Microbiology

Built environment microbiome

Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines – Belen Torondel – Microbial Biotechnology

Efficacy of dental unit waterlines disinfectants on a polymicrobial biofilm – Damien Costa – Water Research

Food microbiology

Warning: contains graphic images: Screening for Viral Pathogens in African Simian Bushmeat Seized at A French Airport – Sarah Temmam – Transboundary and Emerging Diseases

Next-generation sequencing analysis of lager brewing yeast strains reveals the evolutionary history of interspecies hybridization – Miki Okuno – DNA Research

Development of spoilage bacterial community and volatile compounds in chilled beef under vacuum or high oxygen atmospheres – Elina Jääskeläinen – International Journal of Food Microbiology

More microbiology

My favorite structure: Ribosomal small subunit domains radiate from a central core – Burak Gulen – Scientific Reports

Selection favors incompatible signaling in bacteria – Alfonso Pérez-Escudero – PNAS

Microbes in the news

Bacteria Can Convey Electrical Messages the Same Way Neurons Do – Diana Kwon – Scientific American

40 Trillion Bacteria on and in Us? Fewer Than We Thought – Nicholas Bakalar – New York Times

Scientists discover new microbes that thrive deep in the earth – Phys.org

Europe’s Richest Microbiome Biotech Acquires Irish Start-up To Accelerate – Labiotech

There are always bacteria lurking in dental equipment, suggests research – MedicalXpress

Genes, bugs and radiation: WHO backs new weapons in Zika fight – Ben Hirschler – Reuters

Gene Linked to Patients’ Response to Infectious Diseases – GenEngNews

Science, publishing, and career

Poisoning your lab mates? Simulating Scientific Sabotage, For Fun: With a card game, researchers make light of the “wacky aspects of scientific research.” – Tracy Vence – The Scientist

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February 13, 2016

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Fungal communities of bark beetles, microbiome in rhinosinusitis, deep-sea chemolithoautotrophic communities, talking walls (microbes in houses), and, for Valentine’s Day: cocoa bean fermentation. 

Jobs and events

Postdoc opportunity, University of Notre Dame: 20,000 longitudinal gut microbiome samples from wild baboons

Pregnancy and birth

Review: Prevention of Necrotizing Enterocolitis Through Manipulation of the Intestinal Microbiota of the Premature Infant – Kannikar Vongbhavit – Clinical Therapeutics

Human oral microbiome

Analysis of bacterial community profiles of endodontically infected primary teeth using pyrosequencing – Kwan Hee Yun – International Journal of Paediatric Dentistry

Human respiratory microbiome

Composition and dynamics of the respiratory tract microbiome in intubated patients – Brendan J. Kelly – Microbiome Journal

Metagenomic Sequencing of the Chronic Obstructive Pulmonary Disease Upper Bronchial Tract Microbiome Reveals Functional Changes Associated with Disease Severity – Simon J. S. Cameron- PLOS ONE

The bacterial microbiome in chronic rhinosinusitis: Richness, diversity, postoperative changes, and patient outcomes – Edward John Cleland – American Journal of Rhinology & Allergy

Review: Microbiome of the paranasal sinuses: Update and literature review – Jivianne T. Lee – American Journal of Rhinology & Allergy

Editorial: The microbiome of the sinuses and its relevance in health and disease – Simon A. Carney

Human reproductive tract microbiome

Molecular detection of intrauterine microbial colonization in women with endometriosis – Khaleque N. Khan – European Journal of Obstetrics & Gynecology and Reproductive Biology

Review: The Basics of Bacteriuria: Strategies of Microbes for Persistence in Urine – Deepak S. Ipe – Frontiers in Cellular and Infection Microbiology

Review: The Human Microbiome during Bacterial Vaginosis – Andrew B. Onderdonk – Clinical Microbiology Reviews

Human gut microbiome

Allergy associations with the adult fecal microbiota: Analysis of the American Gut Project – Xing Hua – EBioMedicine

An Integrated Metabolomic and Microbiome Analysis Identified Specific Gut Microbiota Associated with Fecal Cholesterol and Coprostanol in Clostridium difficile Infection – Vijay C. Antharam – PLOS ONE

Review: The Role of Probiotics on the Microbiota: Effect on Obesity – Esther Nova – Nutrition in Clinical Practice

Editorial: Policing of gut microbiota by the adaptive immune system – Laurent Dollé – BMC Medicine

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

Perspective: The Second Brain: Is the Gut Microbiota a Link Between Obesity and Central Nervous System Disorders? – Javier Ochoa-Repáraz – Current Obesity Reports

Review: Butyrate, Neuroepigenetics and the Gut Microbiome: Can a High Fiber Diet Improve Brain Health? – Megan W. Bourassa – Neuroscience Letters

Gut passage

Colonic response to laxative ingestion as assessed by MRI differs in constipated irritable bowel syndrome compared to functional constipation – C. Lam – Neurogastroenterology & Motility

How do primates affect seed germination? A meta-analysis of gut passage effects on neotropical plants – Lisieux F. Fuzessy – Oikos

Models of microbiome research

Drosophila: Effects of co-occurring Wolbachia and Spiroplasma endosymbionts on the Drosophila immune response against insect pathogenic and non-pathogenic bacteria – Upasana Shokal – BMC Microbiology

Rats: Diet-induced changes in maternal gut microbiota and metabolomic profiles influence programming of offspring obesity risk in rats – Heather A. Paul – Scientific Reports

Thesis, mice: The effects of nicotine on the gut microbiome and the serum metabolite profile of mice – Ridwan Amin Mahbub – University of Georgia

Contains several cases of image duplication (might be error): Dietary Fiber Intake Regulates Intestinal Microflora and Inhibits Ovalbumin-Induced Allergic Airway Inflammation in a Mouse Model – Zhiyu Zhang – PLOS ONE

Animal microbiome

Metabarcoding of fungal communities associated with bark beetles – Kirsten E. Miller – Ecology and Evolution

Deep 16S rRNA gene sequencing of anterior foregut microbiota from the blue-green sharpshooter (Graphocephala atropunctata) – E. E. Rogers – Journal of Applied Entomology

A bacterial filter protects and structures the gut microbiome of an insect – Michele Caroline Lanan – The ISME Journal

Plant, root, and soil microbiome

Isolation and Identification of Plant Growth Promoting Rhizobacteria from Cucumber Rhizosphere and Their Effect on Plant Growth Promotion and Disease Suppression – Shaikhul Islam – Frontiers in Microbiology

Microbial biomass and soil organic carbon accumulation on a former lakebed near Novosibirsk, Russia – Mikhail. V. Yakutin – Journal of Plant Nutrition and Soil Science

A cost-effective and efficient strategy for Illumina sequencing of fungal communities: A case study of beech endophytes identified elevation as main explanatory factor for diversity and community composition – A.B. Siddique – Fungal Ecology

Primer: Networking in the Plant Microbiome – Marcel G. A. van der Heijden – PLOS Biology

Thesis: Next generation sequencing on soil samples from Etosha National Park: Diversity studies of an anthrax reservoir – Valseth, Karoline

Water and extremophile microbiome

Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent – Caroline S Fortunato – The ISME Journal

Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt – Sean P Jungbluth – The ISME Journal

Context dependency in biodiversity patterns of central German stream metacommunities – Jonathan D. Tonkin – Freshwater Biology

Microbial community composition in the marine sediments of Jeju Island: next-generation sequencing surveys – Heebok Choi – Journal of Microbiology and Biotechnology

Effects of temperature stress and aquarium conditions on the red macroalga Delisea pulchra and its associated microbial community – Enrique Zozaya-Valdés – Frontiers in Microbiology

Using in situ bacterial communities to monitor contaminants in river sediments – Yuwei Xie – Environmental Pollution

DGGE: Effects of fullerene (C60), multi-wall carbon nanotubes (MWCNT), single wall carbon nanotubes (SWCNT) and hydroxyl and carboxyl modified single wall carbon nanotubes on riverine microbial communities – J. R. Lawrence – Environmental Science and Pollution Research

Built environment microbiome

Walls talk: Microbial biogeography of homes spanning urbanization – Jean F. Ruiz-Calderon – Science Advances

Microbial communities affecting albumen photography heritage: a methodological survey – Andrea Puškárová – Scientific Reports

Food microbiology

Characterization of microbiota in Plaisentif cheese by high-throughput sequencing –
Alessandra Dalmasso – LWT-Food Science and Technology

Metagenomic analysis of viruses associated with field-grown and retail lettuce identifies human and animal viruses – Tiong Gim Aw – International Journal of Food Microbiology

Bacterial diversity of floor drain biofilms and drain waters in a Listeria monocytogenes contaminated food processing environment – Monika Dzieciol

Review: The cocoa bean fermentation process: from ecosystem analysis to starter culture development – L. De Vuyst – Journal of Applied Microbiology

Techniques

Oufti: an integrated software package for high-accuracy, high-throughput quantitative microscopy analysis – Ahmad Paintdakhi – Molecular Microbiology

Viruses and phages

Perspective: A Virological Perspective on Cancer – Blossom Damania – PLOS Pathogens

Bioinformatics and metagenomics

Fast search of thousands of short-read sequencing experiments – Brad Solomon – Nature Biotechnology

Open-Source Sequence Clustering Methods Improve the State Of the Art – Evguenia Kopylova

Editorial: Bacterial Speciation: Genetic Sweeps in Bacterial Species -Frederick M. Cohan – Current Biology

Microbes in the news

Walls talk – or at least hold many secrets a wall whisperer can reveal – Jonathan Eisen – MicroBEnet

Country microbes, city microbes—where you live can change how you get sick – Annalee Newitz – Ars Technica

Urbanization Leads to Change in Type of Bacteria in the Home – Lauran Neergaard – ABC News

Fun list: Ranking the Top 10 Best Bacteria on Earth – Ben Guarino – Inverse

Science, publishing and career

The Research Pirates of the Dark Web – Kaveh Waddell  – The Atlantic

Researcher illegally shares millions of science papers free online to spread knowledge – Science Alert

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February 12, 2016

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Infant gut microbiota development and family foods, a paper on the “blood microbiome” that caused some discussion on Twitter, Penicillinum and pears, and community types in the human microbiome.

Jobs and events

Mothur and programming in R workshop, May 23-25, Detroit

Postdoctoral Research Assistant – Microbiome – University of Oxford – Department of Plant Sciences

Pregnancy and birth

Infant Gut Microbiota Development Is Driven by Transition to Family Foods Independent of Maternal Obesity – Martin Frederik Laursen – mSphere

Human gut

A Novel Microbiome Therapeutic Increases Gut Microbial Diversity and Prevents Recurrent Clostridium difficile Infection – Sahil Khanna – The Journal of Infectious Diseases

Microbiome of blood

No carefully designed controls, no deposit of sequence reads, misleading Y-axis in Figure S1. I don’t endorse this study: Comprehensive description of blood microbiome from healthy donors assessed by 16S targeted metagenomic sequencing – Sandrine Païssé – Transfusion

Animal models

Rearing room affects the non-dominant chicken caecum microbiota, while diet affects the dominant microbiota – Jane Ludvigsen – Frontiers in Veterinary Science

Extremophiles and water microbiome

Artificial electron acceptors decouple archaeal methane oxidation from sulfate reduction – Silvan Scheller – Science

Perspective: A new diet for methane oxidizers – Amelia-Elena Rotaru – Science

The role of particle associated microbes in remineralization of fecal pellets in the upper mesopelagic of the Scotia Sea, Antarctica – Anna Belcher – Limnology and Oceanography

Growth dynamics of a laminated microbial mat in response to variable irradiance in an Antarctic lake – Ian Hawes – Freshwater Biology

Food microbiology

Profile of Penicillium species in the pear supply chain – I. Scholtz – Plant Pathology

More microbes

Survival games at the dinner table: regulation of Enterobacterial virulence through nutrient sensing and acquisition – Gaëlle Porcheron – Current Opinion in Microbiology

Bioinformatics and metagenomics

On the Origins and Control of Community Types in the Human Microbiome – Travis E. Gibson – PLOS Computational Biology

Microbes in the news

Forget chocolates. Give your sweetheart mushrooms this Valentine’s Day, says Stanford scientist – Rosemary Mena-Werth – Stanford News

Infant gut microbiome development not driven by maternal weight – Stephen Feller – UPI

Solid foods take over shaping of gut microbiota by 9 months – Yvette Brazier – Medical News Today

Why we might need to kill Australia’s koalas: Chlamydia infection is running rampant through their population, and a controlled cull might be their best hope- Katie Silver – BBC

Researchers Believe That Socialization Helps Spread Beneficial Gut Bacteria – Shariqua Ahmed – DogoNews

Novel microbiome therapy appears to prevent recurrent C. difficile infection – Healio

AbbVie Launches IBD Collaboration with Synlogic – GenEngNews

Bik’s Picks

Thursday’s massive gravitational wave news was broken by a sheet cake (really) – Rachel Feltman – Washington Post

Science and art

An Artist Asks: Whose Business Is Our DNA? – Short film on artwork by Heather Dewey-Hagborg who created masks of strangers based on genetic material left behind – 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 8, 2016

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Plasmid-mediated salt tolerance in the gut microbiota, Tuft cells and immunity, microbes of the Cerrado, impact of sequencing technique on microbiota analysis, and a new microbiome tool on the cloud.

Events

Introducing Nephele, NIAID’s new cloud-based microbiome analysis tool. Webinar on March 7. See also under Bioinformatics below.

Human oral microbiome

Research highlight: FISHing in the oral microbiota – Naomi Attar – Nature Reviews Microbiology

Human gut microbiome

Intestinal microbiota in inflammatory bowel disease and carcinogenesis: Implication for therapeutics – Steven D. Bruner – Clinical Pharmacology & Therapeutics

Evidence for plasmid mediated salt tolerance in the human gut microbiome and potential mechanisms – Eileen Broaders – FEMS Microbiology Ecology

Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with IBD – Thomas Lee – Gut

Review: Novel Strategies for Applied Metagenomics – Moore-Connors, Jessica M. – Inflammatory Bowel Diseases

Research highlight: ntestinal microbiota in inflammatory bowel disease and carcinogenesis: Implication for therapeutics – Steven D. Bruner – Clinical Pharmacology & Therapeutics

Models of microbiome research

Tuft cells, taste-chemosensory cells, orchestrate parasite type 2 immunity in the gut – Michael R. Howitt – Science

Effects of dietary resistant starch content on metabolic status, milk composition, and microbial profiling in lactating sows and on offspring performance – H. Yan – Journal of Animal Physiology and Animal Nutrition

Beneficial Effects of Fecal Microbiota Transplantation on Ulcerative Colitis in Mice – Zhihui Tian – Digestive Diseases and Sciences

Plant, root, and soil microbiome

Soil bacterial communities associated with natural and commercial Cyclopia spp. – Anneke Postma – FEMS Microbiology Ecology

Diversity and functional traits of culturable microbiome members, including cyanobacteria in the rice phyllosphere – Siddarthan Venkatachalam – Plant Biology

Microbial Diversity in Cerrado Biome (Neotropical Savanna) Soils – Alinne Pereira de Castro – PLOS ONE

Dissipation and effects of tricyclazole on soil microbial communities and rice growth as affected by amendment with alperujo compost – M. García-Jaramillo – Science of The Total Environment

Opinion: Plant microbiota affects seed transmission of phytopathogenic micro-organisms – Matthieu Barret – Molecular Plant Pathology

Built environment microbiome

Indoor microbial communities: Influence on asthma severity in atopic and nonatopic children – Karen C. Dannemiller – The Journal of Allergy and Clinical Immunology

Antibiotics in drinking water in Shanghai and its contribution to antibiotic exposure of school children – Hexing Wang – Environmental Science & Technology

Pollution and waste microbiology

Characterisation of biofilm and planktonic bacterial and fungal communities transforming high molecular weight polycyclic aromatic hydrocarbons – Benjamin D Folwell – Applied and Environmental Microbiology

Shift in antibiotic resistance gene profiles associated with nanosilver during wastewater treatment – Yanjun Ma – FEMS Microbiology Ecology

Evaluating the Metal Tolerance Capacity of Microbial Communities Isolated from Alberta Oil Sands Process Water – Mathew L. Frankel- PLOS ONE

Nutrient and metal pollution of the eastern Gulf of Finland coastline: Sediments, macroalgae, microbiota – Yulia Gubelit – Science of the Total Environment

Impacts of pristine and transformed Ag and Cu engineered nanomaterials on surficial sediment microbial communities appear short-lived – Joe D Moore – Environmental Science & Technology

Food microbiology

Diversity and Stability of Lactic Acid Bacteria in Rye Sourdoughs of Four Bakeries with Different Propagation Parameters – Ene Viiard – PLOS ONE

Techniques

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis – Adam G. Clooney – PLOS ONE

Don’t put all your eggs in one basket: a cost-effective and powerful method to optimize primer choice for rRNA environmental community analyses using the Fluidigm Access Array – Shawn P. Brown – Molecular Ecology Resources

Probiotics

Probiotic and Functional Characterization of Bifidobacteria of Indian Human Origin – Nancy Awasti – Journal of Applied Microbiology

Bioinformatics

Nephele, microbiome analysis without boundaries. NIAID’s new tool offering cloud-based storage, file transfer, and analysis.

Note: 16S is not the same as metagenomics: Vikodak – A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets – Sunil Nagpal – PLOS ONE

Microbes in the news

Smart Science: Wolbachia Bacteria Might Stop Zika and Dengue Viruses – Judy Stone – Forbes

The science of treating depression during pregnancy – Josie Glausiusz – Quartz

GIANTmicrobes – When Teachers Throw Things – Anne Estes

Gut bacteria may influence alcoholics’ liver damage – Kathryn Doyle – Reuters
Scientists Seek Answers on Zika in Other Viruses – Carl Zimmer – New York Times

Bears’ Hibernation Linked To Unusual Changes In Their Gut Microbes – Samantha Mathewson – Nature World News

Bears hibernate ‘with bacterial help’ – Jonathan Webb – BBC News

The Tardigrade story a.k.a. Open Science Wins – Surya Saha – Storify

This Bacteria-Powered Microrobot Navigates via Electric Fields – Michael Byrne – Motherboard

Sainsbury’s Recall Camembert Cheese Products Over Food Poisoning Concerns – Natasha Hinde – The Huffington Post UK

EFSA update: Fully defining microbiota cause-and-effect: Yolanda Sanz provides update –
Will Chu – Nutraingredients

Satire: Trump Proposes Ban On All Microbiome Researchers “Until We Know What They Are Up To” “When I become president, we are going to make American poo great once again.” – The Allium

Bacteria Hysteria

What’s hiding in your handbag? Contact 6 tests purses for bacteria – Katrina Cravy – Fox

Bik’s Picks

Natural History Museums Are Teeming With Undiscovered Species – Ed Yong – The Atlantic

New species of tarantula found near Folsom Prison named for Johnny Cash – Rachel Feltman – Washington Post

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