Category Archives: Plant Root Soil microbiome

September 10, 2016

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Bifidobacteria and ulcerative colitis, the pollen microbiome, busting the 5-second rule, resistance genes in 23,000 microbial genomes, and a cool video of evolution of bacterial resistance.

Events

Gut health, microbiota & probiotics throughout the lifespan – Metabolic & Brain function 2016 – Sept 15-16, Harvard Medical School, Boston, MA

Human oral microbiome

Deep sequencing reveals microbiota dysbiosis of tongue coat in patients with liver carcinoma – Haifeng Lu – Scientific Reports

Human respiratory microbiome

Review: The microbiome in asthma – Magali Noval Rivas – Current Opinion Pediatrics

Human gut microbiome

Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers – Sabrina Duranti – FEMS Microbiology Ecology

Review: Gut Microbiota, Inflammation, and Colorectal Cancer – Caitlin A. Brennan – Annual Review of Microbiology

Review: Microbiota—myeloid cell crosstalk beyond the gut – Sayeh Gorjifard – Journal of Leukocyte Biology

Four reviews in Current Pharmaceutical Design in the category “Could the gut microbiota perhaps be involved in disease X?” – with 4 different X’s. 

Animal models

Antibiotic Treatment Induces Long-lasting Changes in the Fecal Microbiota that Protect Against Colitis – Naomi L. Ward – Inflammatory Bowel Diseases

Differences In CD8αα And Cecal Microbiome Community During Proliferation And Late Cytolytic Phases Of Marek’s Disease Virus (MDV) Infection Are Associated With Genetic Resistance To Marek’s Disease – Sudeep Perumbakkam – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Bacterial microbiota associated with flower pollen is influenced by pollination type, and shows a high degree of diversity and species-specificity – Binoy Ambika Manirajan – Environmental Microbiology

Land use intensification in the humid tropics increased both alpha and beta diversity of soil bacteria – Teotonio Soares de Carvalho – Ecology

Small-scale spatial heterogeneity of ecosystem properties, microbial community composition and microbial activities in a temperate mountain forest soil – Martina Štursová – FEMS Microbiology Ecology

Extremophile microbiome

Seasonal dynamics of extremely halophilic microbial communities in three Argentinian salterns – Leonardo Di Meglio – FEMS Microbiology Ecology

Built environment microbiome

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Christin Lola / Fotolia (via Science Direct)

Longer Contact Times Increase Cross-Contamination of Enterobacter aerogenes from Surfaces to Food – Robyn C. Miranda – Applied and Environmental Microbiology

Researchers debunk ‘five-second rule’: Eating food off the floor isn’t safe. Sometimes bacteria transfer in less than a second – Science Daily

Forget the ‘five-second rule’: Food dropped on the floor picks up bacteria in just ONE second – David Gardner – Daily Mail

Antimicrobial Chemicals Are Associated with Elevated Antibiotic Resistance Genes in the Indoor Dust Microbiome – Erica M. Hartmann – Environmental Science & Technology

Antibiotic Resistance Genes in Indoor Dust – Technology Networks

Metagenomics and bioinformatics

The transfer network of bacterial mobile resistome connecting animal and human microbiome – Yongfei Hu – Applied and Environmental Microbiology

Catalog of Mobile Antibiotic Resistance Genes Helps Explain Transfer to Human Pathogens – Genome Web

Chinese investigators characterize the world of resistance gene exchange among bacteria – Phys.org

Phages and viruses

Bacteriophages in clinical samples can interfere with microbiological diagnostic tools – Maryury Brown-Jaque – Scientific Reports

Techniques

Absolute quantification of microbial taxon abundances – Ruben Props – The ISME Journal

Microbes in the news

Jo Handelsman of White House Office of Science and Technology to Speak Monday – University of Tennessee

WATCH: Bacteria Invade Antibiotics And Transform Into Superbugs – Angus Chen – NPR
This might be the coolest visualization of evolution ever. Watch these bacteria evolve antibiotic resistance in just 12 days – Brian Resnick – Vox

These researchers would like you to mail them your gut bacteria – Katherine Lindemann – Research Gate Blog

Hepatitis A Outbreak Linked to Strawberries at Smoothie Chain – Daniel Victor – New York Times

Bacteria Hysteria

M&S becomes first supermarket to offer anti-bacterial shopping bags to banish bugs such as E. coli –  Katie Morley – The Telegraph

Bik’s non-microbiology Picks

Microbiome analysis, please! Giraffes aren’t just giraffes. Turns out there are four species – Rachel Feltman – Washington Post

Flatworm parasite named after Barack Obama: Is that a compliment? – Rowena Lindsay Christian Science Monitor

 

September 6, 2016

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Tongue diagnostics and bacterial communities, microbiome and ALS, flowers and bees sharing microbes, and CRISPR assembly.

Events

4th World Congress on Targeting Microbiota is organized at Institut Pasteur, Paris, France – October 17-19, 2016

How the Indoor Microbiome Influence Health, with Jack A. Gilbert – October 27, 2016 at British International School of Chicago – Lincoln Park in Chicago

Human oral microbiome

Bacillus as a potential diagnostic marker for yellow tongue coating – Juan Ye – Scientific Reports

Human skin microbiome

Redefining the Chronic-Wound Microbiome: Fungal Communities Are Prevalent, Dynamic, and Associated with Delayed Healing – Lindsay Kalan – mBio

Human respiratory tract microbiome

Review: Development of the respiratory tract microbiota in cystic fibrosis – Emma M. de Koff – Current Opinion in Pulmonary Medicine

Human urinary tract microbiome

Commentary: “Urinary tract infection” and the microbiome – Thomas E. Finucane – The American Journal of Medicine

Human gut microbiome

Pitfalls in Inferring Human Microbial Dynamics from Temporal Metagenomics Data – Hong-Tai Cao – bioRxiv

Evaluation of the microbial diversity in amyotrophic lateral sclerosis using high-throughput sequencing – Xin Fang – Frontiers in Microbiology

Review: Beyond 16S rRNA community profiling: intra-species diversity in the gut microbiota – Kirsten M. Ellegaard – Frontiers in Microbiology

Review: Epigenetic mechanisms in microbial members of the human microbiota: current knowledge and perspectives – Natacha Cureau – Future Medicine

Microbiology and immunology

Perspective: Autoimmunity and the microbiome: T-cell receptor mimicry of “self” and microbial antigens mediates self tolerance in holobionts – Robert Root-Bernstein – BioEssays

Animal models of microbiome research

Ketogenic diet modifies the gut microbiota in a murine model of autism spectrum disorder – Christopher Newell – Molecular Autism

Animal microbiome

Disentangling a holobiont – recent advances and perspectives in Nasonia wasps – Jessica Dittmer – Frontiers in Microbiology

Review: The terrestrial isopod microbiome: An all-in-one toolbox for animal-microbe interactions of ecological relevance – Didier Bouchon – Frontiers in Microbiology

Plant, root, and soil microbiome

Microbial communities in passive remediation systems at three abandoned coal mine sites in the United Kingdom – Carmen Falagán – Proceedings IMWA 2016, Freiberg

Primary Succession of Nitrogen Cycling Microbial Communities Along the Deglaciated Forelands of Tianshan Mountain, China – Jun Zeng – Frontiers in Microbiology

Flowers and Wild Megachilid Bees Share Microbes – Quinn S. McFrederick – Microbial Ecology

Triclosan Resistome from Metagenome Reveals Diverse Enoyl Acyl Carrier Protein Reductases and Selective Enrichment of Triclosan Resistance Genes – Raees Khan – Scientific Reports

Water and extremophile microbiome

Oligotrophic Lagoons of the South Pacific Ocean Are Home to a Surprising Number of Novel Eukaryotic Microorganisms – Eunsoo Kim – Environmental Microbiology

Upstream freshwater and terrestrial sources are differentially reflected in the bacterial community structure along a small Arctic river and its estuary – Aviaja L. Hauptmann – Frontiers in Microbiology

Built environment microbiology

Review: Emerging Investigators Series: Sewer surveillance for monitoring antibiotic use and prevalence of antibiotic resistance: urban sewer epidemiology – Nicole Fahrenfeld – Environmental Science: Water Research & Technology

Food microbiology

High-throughput identification of the microbial biodiversity of cocoa bean fermentation by MALDI-TOF MS – S. Miescher Schwenninger – Letters in Applied Microbiology

Bioinformatics and metagenomics

Assemble CRISPRs from metagenomic sequencing data – Jikai Lei – Bioinformatics

Contig annotation tool CAT robustly classifies assembled metagenomic contigs and long sequences – Diego D. Cambuy – bioRxiv

Techniques

High throughput sequencing of multiple amplicons for barcoding and integrative taxonomy – Perrine Cruaud – bioRxiv

Microbes in the news

Podcast (12 min) with Stephen Pointing: Protecting the Earth’s Microbiome – Jesse Mulligan – Radio NZ

Biochemists’ discovery could lead to vaccine against ‘flesh-eating’ bacteria – Science Daily

Enzyme from oral bacteria could be potential therapy for celiac disease – News Medical

Bik’s Non-Microbiology Picks

Bizarre ant colony discovered in an abandoned Polish nuclear weapons bunker – Annalee Newitz – ArsTechnica

September 5, 2016

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A microbial ecosystem created by fracking.

Human gut microbiome

Note: “All 34 PD patients were on dopaminergic drugs” Short chain fatty acids and gut microbiota differ between patients with Parkinson’s disease and age-matched controls – Marcus M. Unger – Parkisonism & Related Diseases

Effects of Proton Pump Inhibitors on the Gastric Mucosa-Associated Microbiota in Dyspeptic Patients – Francesco Paroni Sterbini – Applied and Environmental Microbiology

Upcoming study: Influence of habitual dietary fibre intake on the responsiveness of the gut microbiota to a prebiotic: protocol for a randomised, double-blind, placebo-controlled, cross-over, single-centre study – Genelle Healey – BMJ Open

Plants, roots, and soil microbiome

Screen Shot 2016-09-05 at 2.12.43 PMMicrobial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales – Rebecca A. Daly – Nature Microbiology

Press: New genus of bacteria found living inside hydraulic fracturing wells – ‘Frackibacter’ one of dozens of microbes forming sustainable ecosystems there, study finds – EurekAlert

Air microbiology

Aerobiology of the built environment: Synergy between Legionella and fungi – Absar Alum – American Journal of Infection Control

Generic aspects of the airborne spread of human pathogens indoors and emerging air decontamination technologies – M. Khalid Ijaz – American Journal of Infection Control

Water treatment microbiology

A modified weighted mixture model for the interpretation of spatial and temporal changes in the microbial communities in drinking water reservoirs using compositional phospholipid fatty acid data – I. Stanimirova – Talanta

Point-of-use Unit Based on Gravity Ultrafiltration Removes Waterborne Gastrointestinal Pathogens from Untreated Water Sources in Rural Communities – Cristóbal Chaidez – Wilderness & Environmental Medicine

Bioinformatics

MMinte: an application for predicting metabolic interactions among the microbial species in a community – Helena Mendes-Soares – BMC Bioinformatics

Microbes in the news

Chickenpox Cases In The US Down Since 2-Dose Vaccine Program Began – Dianne Depra – Tech Times

Study shows that more people carry meningitis bacteria than previously thought – Meningitis Research Foundation

Respect the old but seek out the new: Direct 16S rRNA-seq from bacterial communities – Kelle Freel – The Molecular Ecology

Bacterial Leaf Streak, a new corn disease hitting Kansas – Vincent Marshall – Dodge City Daily Globe

Manuka proves best bacteria fighter – Rush and Mills, Whangaroa College students, investigated manuka (tea tree) oil, won a top prize at the recent Top Energy Far North Science and Technology Fair.– Stuff.co.nz

Fears CSIRO staff exposed to ‘low risk’ toxic bacteria at Canberra lab – ABC Australia

Microbes and you: a partnership millions of years old – Dyani LewisCosmos Magazine

September 3, 2016

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The gut microbiome of the American cockroach is as resilient as its host, two papers on polar microbes and climate changes, two JAMA papers about transcription-based tests to distinguish viral from bacterial infections in children, and sampling Jeremy Bentham’s preserved body.

Events

7th edition of the International Course in Microbial Ecology – Publishing Dos and Don’ts for Microbial Ecologists – October 2016, Catania, Italy

Human vaginal microbiome

Alterations of the vaginal microbiota in the third trimester of pregnancy and pPROM –
C. Genovese – Eur Rev Med Pharmacol Sci

Human gut microbiome

Review: The gut microbiota: A treasure for human health – Daotong Li – Biotechnology Advances

Editorial: The Human Gutome: Journey of Microbes and Health – Dimiter Dimitrov – Frontiers in Genetics

Animal microbiome

The core gut microbiome of the American cockroach, Periplaneta americana, is stable and resilient to dietary shifts – Kara A. Tinker – Applied and Environmental Microbiology

Microbiome changes through ontogeny of a tick pathogen vector – Christine P. Zolnik – Molecular Ecology

Plant, root, and soil microbiome

Long-lasting effects of land use history on soil fungal communities in second-growth tropical rain forests – Benedicte Bachelot – Ecological applications

Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers – Sarah M. Allarda – Science of the Total Environment

Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture – Yuan Qin – Biotechnology Advances

Extremophile microbiome

Polar Marine Microorganisms and Climate Change – C. Verde – Advances in Microbial Physiology

Antarctic microbial communities are functionally redundant, adapted and resistant to short term temperature perturbations – S.Z. de Scally – Soil Biology and Biochemistry

Metabolomics and other techniques

The future of NMR-based metabolomics – John L Markley – Current Opinion in Biotechnology

Microfluidics in microbiology: putting a magnifying glass on microbes – Sanya Siddiqui – Integrative Biology

Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass-Spectrometry (MALDI-TOF MS) Based Microbial Identifications: Challenges and Scopes for Microbial Ecologists– Praveen Rahi – Frontiers in Microbiology

More microbiology

Diagnostic Test Accuracy of a 2-Transcript Host RNA Signature for Discriminating Bacterial vs Viral Infection in Febrile Children – Jethro A. Herberg – JAMA

Association of RNA Biosignatures With Bacterial Infections in Febrile Infants Aged 60 Days or Younger – Prashant Mahajan – JAMA

Microbes in the news

The Good Gut: Discussing the stomach’s world of disease-fighting microbes – Paul Costello – Stanford Medicine

San Francisco has a crazy plan to fight pee stink with bacteria-eating enzymes – Urine trouble – Rachel Becker – The Verge

MSU researchers noted for approach to studying bacteria and viruses that live in human gut – Evelyn Boswell – MSU News Service

Yum! Digesting ASM resources for food microbiology – Julie Wolf – American Society for Microbiology

Have you ever wondered what sorts of bacteria and fungi are lurking on Jeremy Bentham? Dr Adam Roberts, thanks to UCL Collections, visited Jeremy Bentham to see if he could find any interesting bacteria. – University College of London

I Contain Multitudes by Ed Yong review – we are possessed by bacteria – Tim Radford – The Guardian

Gaming for Gut Research – American Gut researchers developed Colony B, an app that is both a fun game and a way “citizen scientists” can contribute to microbiome data analysis – UC San Diego Health Sciences News

 

September 2, 2016

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Correlation between oligosaccharides and gut microbes in infants, metabolic pathways in 10 infant twin pairs, an Open-Source alternative for USEARCH, and an important new FDA rule.

Events

Unfortunately, all of the confirmed speakers are men. Nature Conference on Environmental and Human Microbiomes: Drivers of Future Sustainability, February 12-15, 2017, Singapore

Pregnancy and birth

Identification of Oligosaccharides in Feces of Breast-fed Infants and Their Correlation with the Gut Microbial Community – Jasmine C. C. Davis – Molecular & Cellular Proteomics

Membrane Vesicles of Group B Streptococcus Disrupt Feto-Maternal Barrier Leading to Preterm Birth – Manalee Vishnu Surve – PLOS Pathogens

Press: Bacteria linked to stillbirth: mouse study – Sarah Wiedersehn – Australian Associated Press

Diversity of Gut Microbiota Metabolic Pathways in 10 Pairs of Chinese Infant Twins – Shaoming Zhou – PLOS ONE

A preliminary investigation on the relationship between gut microbiota and gene expressions in peripheral mononuclear cells of infants with autism spectrum disorders – Ryo Inoue – Bioscience, Biotechnology, and Biochemistry

Human gut microbiome

Commentary: Gut microbiota: Changes in gut microbes and host metabolism: squaring the circle? – Patrice D. Cani – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Bacterial diversity of the American sand fly Lutzomyia intermedia using high-throughput metagenomic sequencing – Carolina Cunha Monteiro – Parasites & Vectors

Deep COI sequencing of standardized benthic samples unveils overlooked diversity of Jordanian coral reefs in the northern Red Sea – Mamoon M.D. Al-Rshaidat – Genome

Plant, root, and soil microbiome

Metagenomic Analysis of Some Potential Nitrogen-Fixing Bacteria in Arable Soils at Different Formation Processes – Agnieszka Wolińska – Microbial Ecology

Water microbiome

Microbial diversity within the Trichodesmium holobiont – Mónica Rouco – Environmental Microbiology

Bioinformatics and metagenomics

MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures – Samuele Girotto – Bioinformatics

A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units – Matthew A. Jackson – PeerJ

An Open Source alternative for USEARCH: VSEARCH: a versatile open source tool for metagenomics – Torbjørn Rognes- PeerJ Preprint

Using viromes to predict novel immune proteins in non-model organisms – Steven D. Quistad – Proceedings of the Royal Society B

Microbes in the news

FDA issues final rule on safety and effectiveness of antibacterial soaps. Rule removes triclosan and triclocarban from over-the-counter antibacterial hand and body washes – FDA

FDA bans antibacterial soaps; “No scientific evidence” they’re safe, effective
Ban includes soaps with any of 19 chemicals, including triclosan – Beth Mole – ArsTechnica

Living Russian Dolls.They have bacteria in their cells, and smaller bacteria in those bacteria—and that’s not even the weirdest bit – Ed Yong – The Atlantic

Sydney scientists accidentally discover antibiotic to treat koalas with chlamydia – Matt Wordsworth – ABC Australia

High Demand For Antibiotics Leads To Growth In Microbiology Culture Industry In United States – MedGadget

September 1, 2016

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Bedouins, urban Saoudis and monkeys, a subglacial lake, and the oldest microbial fossils.

Events

Alfred P. Sloan Foundation Workshop on Viruses to be Held in Singapore, January 2017 – David Coil – MicroBEnet

Human respiratory microbiome

News: Does barnyard dust protect Amish children from asthma? – Bryant Furlow – The Lancet

Human gut microbiome

Gut microbiome and dietary patterns in different Saudi populations and monkeys – Emmanouil Angelakis – Scientific Reports

Fecal Microbiota Transplantation is Safe and Efficacious for Recurrent or Refractory Clostridium difficile Infection in Patients with Inflammatory Bowel Disease – Monika Fischer

Animal experiments

High fat diet drives obesity regardless the composition of gut microbiota in mice – Sylvie Rabot – Scientific Reports

Gut Microbiota Promote Angiotensin II–Induced Arterial Hypertension and Vascular Dysfunction – Susanne H. Karbach – Hypertension

Plant, root, and soil microbiome

Forest area and connectivity influence root-associated fungal communities in a fragmented landscape – Rachel L. Vannette – Ecology

Review: Comparative phylogenomics of symbiotic associations – Pierre-Marc Delaux – New Phytologist

Water and extremophile

Microbial Community Structure of Subglacial Lake Whillans, West Antarctica – Amanda M. Achberger – Frontiers in Microbiology

Dust microbiome

Poultry houses: DNA from dust: comparative genomics of large DNA viruses in field surveillance samples – Utsav Pandey – bioRxiv

Techniques

Direct 16S rRNA-seq from bacterial communities: a PCR-independent approach to simultaneously assess microbial diversity and functional activity potential of each taxon – Riccardo Rosselli – Scientific Reports

More microbiology

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Geological map and location of microbial structures

Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures – Allen P. Nutman – Nature

Press: Life thrived on young Earth: scientists discover 3.7-billion-year-old fossils – Science Daily
The World’s Oldest Fossils Are 3.7 Billion Years Old. The newly discovered rocks suggest that life arose very quickly after the Earth was formed – Ed Yong – The Atlantic

Microbes in the news

Microbial genomics and the future of food microbiology – Julie Wolf – American Society for Microbiology

Space Microbiome? Yes Please! and I’ll take a minION sequencer as well if you don’t mind – Ben Libberton – NPJ Biofilms Community

Multitalented microbiology student is highly lauded for her scholarship – Western Michigan University

Manuka honey makes bacteria less resistant to antibiotics – Rowena Jenkins – The Conversation

Changes in Gut microflora – early warning of Equine Metabolic Syndrome (EMS)? – Jackie Bellamy-Zions – Harness Link

uBiome Hires New Vice President of Research and Development: Dr. Audrey Goddard Joins from Genomic Health and Genentech – PR Web

Samorost 3’s fairy tale of microbiology is now on iPhone – Chris Priestman – Kill Screen

Science, publishing, and career

How to Motivate Your Employees: Give Them Compliments and Pizza – Melissa Dahl – New York Magazine

Opinion: Fixing Science’s Human Bias. It’s time to accelerate the conversation about why the research community is still not diverse – Edward Courchaine and Sarah Smaga – The Scientist

Thanks to the glass ceiling breakers – Yarrow Axford – Science

Peer review

HT: Tomer Altman: Stupid Patent of the Month: Elsevier Patents Online Peer Review – Electronic Frontier Foundation

Research Integrity

OMICS vs. The FTC: Plagiarism at a Predatory Publisher – Neuroskeptic – Discover

 

August 31, 2016

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ICU, Rudlavibizon, Flickr

Gut microbiota changes in the ICU, air microbiome of the Gobi desert, host response of human cells to gut microbiota.

Event

Synbiobeta SF2016, October 4-6, South San Francisco, CA

Human gut microbiome

Extreme Dysbiosis of the Microbiome in Critical Illness – Daniel McDonald – mSphere

Press: ICU patients lose helpful gut bacteria within days of hospital admission – Science Daily
Tracking Bacterial Imbalance in the ICU – Stephen Ornes -mBiosphere

Review: The human gut microbiome, diet, and health: “post hoc non ergo propter hoc” – Guus Roeselers – Trends in Food Science & Technology

Review: Interplay between gut microbiota, its metabolites and human metabolism: dissecting cause from consequence – A.V. Hartstra – Trends in Food Science & Technology

Animal and other model experiments

Bidirectional communication between the Aryl hydrocarbon Receptor (AhR) and the microbiome tunes host metabolism – Agata Korecka – NPJ Biofilms and Microbiomes

Temporal dynamics of bacterial microbiota in the human oral cavity determined using an in situ model of dental biofilms – Nanako Wake – NPJ Biofilms and Microbiomes

Normalizing Microbiota-Induced Retinoic Acid Deficiency Stimulates Protective CD8+ T Cell-Mediated Immunity in Colorectal Cancer – Nupur Bhattacharya – Immunity

Genetic and Transcriptional Analysis of Human Host Response to Healthy Gut Microbiota – Allison L. Richards – mSystems

Animal microbiome

Whole gut microbiome composition of damselfish and cardinalfish before and after reef settlement – Darren J Parris – PeerJ

Plant, root, and soil microbiome

Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity – Zhilin Yuan – Scientific Reports

A native and an invasive dune grass share similar, patchily distributed, root-associated fungal communities – Renee B. Johansen – Fungal Ecology

Bacterial community structure and function shift across a northern boreal forest fire chronosequence – Hui Sun – Scientific Reports

Water microbiome

Complex bacterial communities in the deep-sea sediments of the Bay of Bengal and volcanic Barren Island in the Andaman Sea – Pankaj Verma – Marine Genomics

Neutral processes and species sorting in benthic microalgal community assembly: effects of tidal resuspension – Craig J. Plante – Journal of Phycology

Air microbiome

Variations in the structure of airborne bacterial communities in Tsogt-Ovoo of Gobi desert area during dust events – Teruya Maki – Air Quality, Atmosphere & Health

Bioinformatics and metagenomics

A phylogenetic transform enhances analysis of compositional microbiota data – Justin D Silverman – bioRxiv

Higher classification sensitivity of short metagenomic reads with CLARK-S – Rachid Ounit – Bioinformatics

GRASPx: efficient homolog-search of short peptide metagenome database through simultaneous alignment and assembly – Cuncong Zhong – BMC Bioinformatics

Microbial ecology

Quantifying human impact on Earth’s microbiome – Stephen B. Pointing – Nature Microbiology

Synthetic microbial ecology and the dynamic interplay between microbial genotypes –
Jan Dolinšek – FEMS Microbiology Reviews

Microbes in the news

Engineered gut bacteria protect mice against obesity, improve liver function – Oliver Worsley – Fierce Biotech

You’re probably not doing metagenomics – Mick Watson – Opiniomics

Mayo Adds To Its List Of Gut Microbiome Startup Collaborators – Don Jacobson – Twin Cities Business

Nice analysis of Tweets from #ISME16 by Keith Turner – Jonathan Eisen – MicroBEnet

Peer review and science misconduct

Recognizing Peer Reviewers: a Webinar to Celebrate Editors and Researchers – September 19, 2016 – Elsevier Publishing Campus

Stop ignoring misconduct – Donald S. Kornfeld & Sandra L. Titus – Nature

Bik’s Non-Microbiology Picks

Paperfuge: An ultra-low cost, hand-powered centrifuge inspired by the mechanics of a whirligig toy – M. Saad Bhamla – bioRxiv

August 29b, 2016

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Male grey cockatiel, Wikipedia

Factors that shape early life microbiome, pet birds, robust ambient temperature storage of stool samples, antibacterial activity of wasabi.

Pregnancy and birth

Joint effects of pregnancy, sociocultural, and environmental factors on early life gut microbiome structure and diversity – Albert M. Levin – Scientific Reports

Human gut microbiome

Theoretical Review: The shift work and health research agenda: Considering changes in gut microbiota as a pathway linking shift work, sleep loss and circadian misalignment, and metabolic disease – Amy C. Reynolds – Sleep Medicine Reviews

Review: Mechanisms of inflammation-driven bacterial dysbiosis in the gut – M Y Zeng – Mucosal Immunology

Animal experiments

Review: Experimental Models to Study the Role of Microbes in Host-Parasite Interactions – Megan A. Hahn – Frontiers in Microbiology

Animal microbiome

Comprehensive Molecular Characterization of Bacterial Communities in Feces of Pet Birds Using 16S Marker Sequencing – Jose F. Garcia-Mazcorro – Microbial Ecology

Effects of environment, dietary regime and ageing on the dengue vector microbiota: evidence of a core microbiota throughout Aedes aegypti lifespan – Mariana Rocha David – Memórias do Instituto Oswaldo Cruz

Plants, roots, and soil microbiome

Visual Comparative Omics of Fungi for Plant Biomass Deconstruction – Shingo Miyauchi – Frontiers in Microbiology

Bacterial Abilities and Adaptation Toward the Rhizosphere Colonization – Lucas D. Lopes – Frontiers in Microbiology

Review: Advances in research on Epichloë endophytes in Chinese native grasses – Hui Song – Frontiers in Microbiology

Water microbiome

Phytoplankton-associated bacterial community composition and succession during toxic diatom bloom and non-bloom events – Marilou P. Sison-Mangus – Frontiers in Microbiology

Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary – Guangshan Wei – Applied Microbiology and Biotechnology

Waste and pollution microbiome

Evaluating robustness of a diesel-degrading bacterial consortium isolated from contaminated soil – Mateusz Sydow – New Biotechnology

Metagenomic analysis of an ecological wastewater treatment plant’s microbial communities and their potential to metabolize pharmaceuticals – Ian N. Balcom – F1000 Research Preprint

Food microbiology

Review: Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing – J. Ronholm – Clinical Microbiology Reviews

Techniques

A robust ambient temperature collection and stabilization strategy: Enabling worldwide functional studies of the human microbiome – Ericka L. Anderson – Scientific Reports

Press: DNA Genotek’s OMNIgene®Ÿ GUT Kit is Proposed as Standardized Test for Worldwide Studies of the Human Microbiome – Globe NewsWire

More microbiology

Antibacterial activities of wasabi against Escherichia coli O157:H7 and Staphylococcus aureus – Zhongjing Lu – Frontiers in Microbiology

Resource Availability Modulates the Cooperative and Competitive Nature of a Microbial Cross-Feeding Mutualism – Tim A. Hoek – PLOS Biology

Microbes in the news

The women who discovered India’s first HIV cases – Geeta Pandey – BBC News

Captivity Makes Monkey Microbiomes More Human-Like – Ed Yong – The Atlantic

Interview with author of The Germ Files – Jason Tetro – Ben Libberton – Nature Microbiology Community

UGent researchers create bacteria that turns organic waste into plastic – Toon Lambrechts – Flanders Today

First DNA Sequencing in Space a Game Changer – NASA

UCSD alumna first to sequence DNA in space – Gary Robbins – San Diego Union Tribune

 

August 27, 2016

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Gut microbiome in pre-Columbian mummies, spacecraft assembly cleanrooms, smokeless tobacco products, time series data, and a return of the Musical Microbes.

Human skin microbiome

Skin fungal community and its correlation with bacterial community of urban Chinese individuals – Marcus H. Y. Leung – Microbiome

Human oral microbiome

High-throughput quantitative method for assessing coaggregation among oral bacterial species – E. Levin-Sparenberg – Letters in Applied Microbiology

Human gut microbiome

Taxonomic and predicted metabolic profiles of the human gut microbiome in pre-Columbian mummies – Tasha M. Santiago-Rodriguez – FEMS Microbiology Ecology

Note: unclear definition of “redemption”; means that a medication prescription was filled. Broad-Spectrum Antibiotic Treatment and Subsequent Childhood Type 1 Diabetes: A Nationwide Danish Cohort Study – Tine D. Clausen – PLOS ONE

Animal experiments

Impact of dietary fibre:starch ratio in shaping caecal archaea revealed in rabbits – Y. Zhu – Journal of Animal Physiology and Animal Nutrition

Plant, root, and soil microbiome

Endolithic microbial diversity in sandstone and granite from the McMurdo Dry Valleys, Antarctica – Stephen D. J. Archer – Polar Biology

Dry Season Constrains Bacterial Phylogenetic Diversity in a Semi-Arid Rhizosphere System – Rodrigo Gouvêa Taketani – Microbial Ecology

Review: Bacteria in decomposing wood and their interactions with wood-decay fungi – Sarah R. Johnston – FEMS Microbiology Ecology

Water microbiome

Multitaxon activity profiling reveals differential microbial response to reduced seawater pH and oil pollution – Francisco J. R. C. Coelho – Molecular Ecology

High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities – Anders Lanzén – Molecular Ecology

Microbial source tracking in impaired watersheds using PhyloChip and machine-learning classification – Eric A. Dubinsky – Water Research

Spacecraft microbiome

Functional metagenomics of spacecraft assembly cleanrooms: Presence of virulence factors associated with human pathogens – Mina Bashir – Frontiers in Microbiology

Tobacco microbiome

Bacterial Populations Associated with Smokeless Tobacco Products – Jing Han – Applied and Environmental Microbiology

Bacteria in smokeless tobacco products may be a health concern – American Society for Microbiology
http://www.asm.org/index.php/journal-press-releases/94525-bacteria-in-smokeless-tobacco-products-may-be-a-health-concern
Proteomics

Development of an Integrated Pipeline for Profiling Microbial Proteins from Mouse Fecal Samples by LC-MS/MS – Jing Wu – Journal of Proteome Research

Bioinformatics, metagenomics, and statistics

Modeling time-series data from microbial communities – Benjamin J Ridenhour – bioRxiv

Improving ancient DNA genome assembly – Alexander Seitz – PeerJ Preprint

More microbiology

The Musical Microbes are back! Influence of a mono-frequency sound on bacteria can be a function of the sound-level – Vijay Kothari – bioRxiv

Microbes in the news

Focus: California drought reducing beach bacteria: Reduced runoff has meant fewer health advisories, data show – Daniel Wheaton – San Diego Union Tribune
Mystery Solved: How Lyme Disease Bacteria Spread Around the Body – Rachael Rettner – LiveScience

In sub-Saharan Africa, cancer can be an infectious disease – ScienceDaily

#BacteriaHysteria: You Should Never Ask For a Slice Of Lemon In Your Drink – Alice Sholl – Yahoo

Science, publishing, and career

There Was A Huge Outpouring Of Support For This Little Girl Who Got Bullied For Loving Bugs. Let Sophia play with her bugs! – Ishmael N. Daro – BuzzFeed

August 26, 2016

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MRI scans of colonic contents in setting of diet or defaecation, fecal transplants, the microbiome of ambulances, and a core taxa tool.

Pregnancy and birth

Longitudinal study on clinical and microbial analysis of periodontal status in pregnancy – Fernanda Campos Machado – Brazilian Oral Research

Review: Role of microbiota function during early life and children neurodevelopment – Tomás Cerdó – Trends in Food Science & Technology

Human oral microbiome (also see above)

Evaluation of oral microbiota in undernourished and eutrophic children using checkerboard DNA-DNA hybridization – M. Testa – Anaerobe

Review: Human neutrophils and oral microbiota: a constant tug-of-war between a harmonious and a discordant coexistence – Silvia M. Uriarte – Immunological Reviews

Human skin microbiome

Temporal stability in chronic wound microbiota is associated with poor healing – Michael Loesche – Journal of Investigative Dermatology

Human gut microbiome

Colonic content: effect of diet, meals, and defecation – R. A. Bendezú – Neurogastroenterology & Motility

Gut microbiota associated with HIV infection is significantly enriched in bacteria tolerant to oxygen – Grégory Dubourg – BMJ Open Gastroenterology

Prevalence and genetic diversity of Blastocystis in family units living in the United States – Pauline D. Scanlan – Infection, Genetics and Evolution

Nitrogen fixation and nifH diversity in human gut microbiota – Katsura Igai – Scientific Reports

Letter: Intestinal Microbiota and Health of Adults Who Were Born by Cesarean Delivery – James J. Goedert – JAMA Pediatrics

Opinion: The microbiome, microbial generated pro-inflammatory neurotoxins, and Alzheimer’s disease – Walter J. Lukiw – Journal of Sport and Health Science

Review: Estrogen and Microbiota Crosstalk: Should We Pay Attention? – Karen L. Chen – Trends in Endocrinology & Metabolism

Review: Gender, aging and longevity in humans: an update of an intriguing/neglected scenario paving the way to a gender-specific medicine – Rita Ostan – Clinical Science

Fecal transplants

Estimating the risks of faecal transplants – K. Patel – The Journal of Hospital Infection

Effect of Fecal Microbiota Transplantation on Recurrence in Multiply Recurrent Clostridium difficile Infection: A Randomized Trial – Colleen R. Kelly – Annals of Internal Medicine

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungi communities from tropical Africa reveal strong ecological structure – Susana Rodríguez-Echeverría – New Phytologist

Gall-ID: tools for genotyping gall-causing phytopathogenic bacteria – Edward W. Davis II – PeerJ

Water microbiome

Structure and function of methanogenic microbial communities in sediments of Amazonian lakes with different water types – Yang Ji – Environmental Microbiology

Built environment microbiome

Detection and characterization of surface microbial contamination in emergency ambulances – Aketza Varona-Barquin – American Journal of Infection Control

Fitness and recovery of bacterial communities and antibiotic resistance genes in urban wastewaters exposed to classical disinfection treatments – Andrea Di Cesare – Environmental Science & Technology

Bioinformatics and metagenomics

PhyloCore: A phylogenetic approach to identifying core taxa in microbial communities – Tiantian Ren – Gene

Microbes in the news

Gut reaction: the surprising power of microbes – Ed Yong – The Guardian

Want to feel better? Be kind to your bugs. Ed Yong’s new book will give you a positive outlook on your body’s trillions of bacteria – Kate Womersley – The Spectator

The world’s largest bacterial study of baby poo – MedicalXpress

What’s in Your Poo? The nonmicrobial components of feces may have important consequences as we try to grapple with microbiome research – Kevin Bonham – Scientific American

Solving a 48-year-old mystery: scientists succeed at growing noroviruses in human intestinal cell cultures in the lab – Graciela Gutierrez – Baylor College of Medicine

MSU researchers spread the buzz about bee viruses – Marshall Swearingen – Montana State University

Science, publishing, and career

Family ties ‘help scientists to get ahead’ in some countries. Levels of nepotism in scientific publishing have been revealed by report – Jack Grove  – Times Higher Education

Supervisors can do a lot more to support PhD students. Many doctoral candidates feel poorly looked after. More awareness and empathy from academics can help fight that – Geoffrey Cantor – Times Higher Education

New leader of NIH’s research watchdog faces staff revolt – Jocelyn Kaiser – Science