Category Archives: Extremophiles

February 24, 2016

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Women in space, cacti, celiac disease, and traveling dust.

Event

Not endorsing – full of quackery and folks trying to sell their books and food supplements, little science: Microbiome Medicine Summit

Human oral microbiome

Review: Porphyromonas gingivalis: An Overview of Periodontopathic Pathogen below the Gum Line – Kah Yan How – Frontiers in Microbiology

Human reproductive tract microbiome

The potential influence of the microbiota and probiotics on women during long spaceflights – Camilla Urbaniak – Future Medicine

Human gut microbiome

Study of duodenal bacterial communities by 16S rRNA gene analysis in adults with active celiac disease versus non celiac disease controls – Esther Nistal – Journal of Applied Microbiology

High Molecular Weight Barley β-Glucan Alters Gut Microbiota Toward Reduced Cardiovascular Disease Risk – Yanan Wang – Frontiers in Microbiology

Review: A glance at … dietary emulsifiers, the human intestinal mucus and microbiome, and dietary fiber – Michael J. Glade – Nutrition

Review: Chemical conversations in the gut microbiota – Jessica A. Thompson – Gut Microbes

Review: Atopic dermatitis and the intestinal microbiota in humans and dogs – J. Mark Craig – Veterinary Medicine and Science

Animal models

Composition of fecal microbiota of laboratory mice derived from Japanese commercial breeders using 16S rRNA gene clone libraries – Ryoko Nozu – Journal of Veterinary Medical Science

Animal microbiome

News in livestock research — use of Omics-technologies to study the microbiota in the gastrointestinal tract of farm animals – Simon Deusch – Computational and Structural Biotechnology Journal

Plant, root, and soil microbiome

The Cacti Microbiome: Interplay between Habitat-Filtering and Host-Specificity – Citlali Fonseca-García – Frontiers in Microbiology

Comparison of Fungal Community in Black Pepper-Vanilla and Vanilla Monoculture Systems Associated with Vanilla Fusarium Wilt Disease –
Wu Xiong – Frontiers in Microbiology

Bacterial-Plant-Interactions: Approaches to Unravel the Biological Function of Bacterial Volatiles in the Rhizosphere – Marco Kai – Frontiers in Microbiology

Short-Term Rhizosphere Effect on Available Carbon Sources, Phenanthrene Degradation, and Active Microbiome in an Aged-Contaminated Industrial Soil – François Thomas – Frontiers in Microbiology

Changes in rhizosphere bacterial gene expression following glyphosate treatment – Molli M. Newman – Science of the Total Environment

Pepino (Solanum muricatum) planting increased diversity and abundance of bacterial communities in karst area – Jinxiang Hu – Scientific Reports

Friend or foe? Biological and ecological traits of the European ash dieback pathogen Hymenoscyphus fraxineus in its native environment – Michelle Cleary – Scientific Report

An interdomain network: the endobacterium of a mycorrhizal fungus promotes antioxidative responses in both fungal and plant hosts – Candida Vannini – New Phytologist

Water and extremophile microbiome

The effect of temperature change on the microbial diversity and community structure along the chronosequence of the sub-arctic glacier forefield of Styggedalsbreen (Norway) – Alejandro Mateos-Rivera – FEMS Microbiology Ecology

Water level changes affect carbon turnover and microbial community composition in lake sediments – Lukas Weise – FEMS Microbiology Ecology

Evaluation of the treatment performance and microbial communities of a combined constructed wetland used to treat industrial park wastewater – Ming Xu – Environmental Science and Pollution Research

Bacterial Composition and Survival on Sahara Dust Particles Transported to the European Alps – Marco Meola – Frontiers in Microbiology

Review: Bridging the divide: a model-data approach to Polar and Alpine microbiology – James A. Bradley – FEMS Microbiology Ecology

Bioinformatics and metagenomics

ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses – Jennifer Fouquier – Microbiome

More microbiology

Peracetic Acid Treatment Generates Potent Inactivated Oral Vaccines from a Broad Range of Culturable Bacterial Species – Kathrin Moor – Frontiers in Immunology

Microbes in the news

Bacteria From the Sahara Desert Found on Swiss Glaciers – Nellie Van Driska – GlacierHub

Wolbachia Bacteria Could Be Answer To Malaria, Dengue: Bill Gates – NDTV

Student Research Focus: Drew Gukeisen discovers and visualizes new virus – Indiana University SouthEast

Bacteria swabbing trend for newborns medically in doubt – Carina Storrs – CNN

Microbes and art

Navel gazing: portraits of the bacteria in our belly buttons – in pictures by Joana Ricou – The Guardian

Science, publishing, and career

Activism: Frustrated postdocs rise up – Paul Smaglik – Nature

Don’t trust an image in a scientific paper? Manipulation detective’s company wants to help – Retraction Watch
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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 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 15, 2016

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Drosophila longevity, gut immunity in insects, metagenomics and beef production, secure computation, and mutualistic phages.

Pregnancy and birth

Research Highlight: Add the microbiota to your birth plan – Cláudio Nunes-Alves – Nature Reviews Microbiology

Human gut microbiome

Review: Gut microbiome and Metabolic Syndrome – Mohsen Mazidi – Diabetes & Metabolic Syndrome: Clinical Research & Reviews

Review: Role of microbes (probiotics and prebiotics) – D.M.A.E. Jonkers – Best Practice & Research Clinical Gastroenterology

Review: Intestinal Microbiota in Liver Disease – Tanvir R. Haque – Best Practice & Research Clinical Gastroenterology

Models of microbiome research

Folate Acts in E. coli to Accelerate C. elegans Aging Independently of Bacterial Biosynthesis – Bhupinder Virk – Cell Reports

Glucose modulates Drosophila longevity and immunity independent of the microbiota – Anthony Galenza – Biology Open

Bacterial successions in the gastrointestinal tract of broilers – Samir Ranjitkar – Applied and Environmental Microbiology

Triclosan Exposure is Associated with Rapid Restructuring of the Microbiome in Adult Zebrafish – Christopher A Gaulke – BioRxiv

Research Highlight: How to extend your stay – Cláudio Nunes-Alves – Nature Reviews Microbiology

Animal microbiome

Review: Gut immunity in Lepidopteran insects – Kai Wu – Developmental & Comparative Immunology

Editorial: Bears Arouse Interest in Microbiota’s Role in Health – Kimberly A. Dill-McFarland – Trends in Microbiology

Plant, root, and soil microbiome

Impact of long-term cropping of glyphosate-resistant transgenic soybean [Glycine max (L.) Merr.] on soil microbiome – Letícia Carlos Babujia – Transgenic Research

Food microbiology

Use of metagenomic shotgun sequencing technology to detect foodborne pathogens within their microbiome in beef production chain – Xiang Yang – Applied and Environmental Microbiology

Microbial dynamics in industrial Blue veined cheeses in different packaging –
P. Duval – International Dairy Journal

Diversity of the microbiota involved in wine and organic apple cider submerged vinegar production as revealed by DHPLC analysis and next-generation sequencing – Janja Trček – International Journal of Food Microbiology

Built environment microbiome

Air dispersed essential oils combined with standard sanitization procedures for environmental microbiota control in nosocomial hospitalization rooms – Fabrizio Gelmini – Complementary Therapies in Medicine

Waste and extremophile microbiology

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

Bioinformatics and metagenomics

Privacy-Preserving Microbiome Analysis Using Secure Computation – Justin Wagner – Bioinformatics

Phages and viruses

Opinion: The Significance of Mutualistic Phages for Bacterial Ecology and Evolution – Nancy Obeng – Trends in Microbiology

Techniques

Unique sequence characteristics account for good DGGE separation of almost full-length 18S rDNAs – Zhiqing Huang – World Journal of Microbiology and Biotechnology

Microbes in the news

New appreciation for human microbiome leads to greater understanding of human health – University of Oklahoma – EurekAlert

From Huts to Cities: How Changes in Dwellings Have Impacted Microbe Exposure for the Human Immune System – New York University Langone

Researchers outline progress in turning bacteria into mini construction workers – The Construction Index

Can we outrun Zika? Walk this street in Colombia and you’ll see how tough it is – Andrew Joseph – STATnews

Cranberries help urinary tract infections, but not as juice – Yvette Brazier – Medical News Today

Biofilm Formation Hampers Removal of Dangerous Bacteria from Hospital Surfaces – Medical Research

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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 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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February 5, 2016

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Just a quick new Digest in the lunch break at the #GamingMetrics conference at UC Davis. Here is a Storify from Day 1 (yesterday) by Jonathan Eisen – more to follow soon.

Pregnancy and birth

Microbial transmission from mothers with obesity or diabetes to infants: an innovative opportunity to interrupt a vicious cycle – Taylor K. Soderborg – Diabetologia

Human urinary tract microbiome

16S rRNA gene-based metagenomic analysis reveals differences in bacteria-derived extracellular vesicles in the urine of pregnant and non-pregnant women – Jae Young Yoo – Experimental & Molecular Medicine

Human gut microbiome

Fungal microbiota dysbiosis in IBD – Harry Sokol – Gut

Animal models of microbiome research

Oxygen Affects Gut Bacterial Colonization and Metabolic Activities in a Gnotobiotic Cockroach Model – Dorothee Tegtmeier – Applied and Environmental Microbiology

Deterministic Assembly of Complex Bacterial Communities in Guts of Germ-Free Cockroaches – Aram Mikaelyan – Applied and Environmental Microbiology

Associations of microbiota and toll-like receptor signaling pathway in esophageal adenocarcinoma – Ali H. Zaidi – BMC Cancer

Comparison of fecal microbiota between German Holstein dairy cows with and without left-sided displacement of the abomasum – Eun-Sik Song – Journal of Clinical Microbiology

Animal microbiome

The Gut Microbiota Modulates Energy Metabolism in the Hibernating Brown Bear Ursus arctos – Felix Sommer – Cell Reports

Plant, root, and soil microbiome

Microbial Diversity in Soil, Sand Dune and Rock Substrates of the Thar Monsoon Desert, India – Subramanya Rao – Indian Journal of Microbiology

Microbial communities play important roles in modulating paddy soil fertility
Xuesong Luo – Scientific Reports

Diversity of archaeal and bacterial communities on exfoliated sandstone from Portchester Castle (UK) – Elisabetta Zanardini – International Biodeterioration & Biodegradation

Distance from the sea as a driving force of microbial communities under water potential stresses in litters of two typical Mediterranean plant species – Anne Marie Farnet Da Silva – Geoderma

Opinion: Back to the future of soil metagenomics – Joseph Nesme – Frontiers in Microbiology

Waste and water treatment

Occurrence and enrichment of ‘bacterial sherpas’: climb to sustainability in wastewater treatment – M. Arnaldos – Water Science & Technology

Metagenomics

Comprehensive Genomic Analyses of the OM43 Clade, Including a Novel Species from the Red Sea, Indicate Ecotype Differentiation among Marine Methylotrophs – Francy Jimenez-Infante – Applied and Environmental Micro

Microbial Ecology

Model-based media selection to minimize the cost of metabolic cooperation in microbial eco-systems – Mattia Zampieri – Bioinformatics

Microbes in the news

Savvy bacteria parents distribute damage unevenly among their children – Cara Giaimo – Atlas Obscura

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