Category Archives: Techniques

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

 

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 25, 2016

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Microbiome of the Graduate Student Gut, allergic cats, tree phyllosphere, milk tanker trucks, and microbes of soda lakes.

Pregnancy and birth

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

General microbiome

Now published after preprint earlier this year and article in Cell: Revised Estimates for the Number of Human and Bacteria Cells in the Body – Ron Sender – PLOS Biology

Enemies and brothers in arms: Candida albicans and gram-positive bacteria – Toni M. Förster – Cellular Microbiology

Human respiratory microbiome

General antibiotic exposure is associated with increased risk of developing chronic rhinosinusitis – Alice Z. Maxfield – The Laryngoscope

Evidence and Role for Bacterial Mucin Degradation in Cystic Fibrosis Airway Disease – Jeffrey M. Flynn – PLOS Pathogens

Human gut microbiome

Master Thesis: Characterizing Microbiome Changes in the Graduate Student Gut – Justin Roy Lund – University of Oklahoma

Altered Fecal Microbiota Correlates with Liver Biochemistry in Nonobese Patients with Non-alcoholic Fatty Liver Disease – Baohong Wang – Scientific Reports

Prosteatotic and Protective Components in a Unique Model of Fatty Liver: Gut Microbiota and Suppressed Complement System – Long Liu – Scientific Reports

Is there a role for stool metabolomics in cystic fibrosis? – Nadeem O Kaakoush – Pediatrics International

Animal microbiome

Allergic to humans? Characterization of the cutaneous mycobiota in healthy and allergic cats using next generation sequencing – Courtney Meason-Smith – Veterinary Dermatology

Fish: The influence of weight and gender on intestinal bacterial community of wild largemouth bronze gudgeon (Coreius guichenoti, 1874) – Xuemei Li – BMC Microbiology

Plant, root, and soil microbiome

Tree phyllosphere bacterial communities: exploring the magnitude of intra- and inter-individual variation among host species – Isabelle Laforest-Lapointe – PeerJ

Long-Term Recovery of Microbial Communities in the Boreal Bryosphere Following Fire Disturbance – Nick A. Cutler – Microbial Ecology

Autochthonous Microbiota in Arsenic-Bearing Technosols from Zemianske Kostoľany (Slovakia) and Its Potential for Bioleaching and Biovolatilization of Arsenic – Alexandra Šimonovičová – Water, Air, & Soil Pollution

Built environment microbiology

Fungi and Bacteria in Indoor Cultural Heritage Environments: Microbial-related Risks for Artworks and Human Health – Enza Di Carlo – Environment and Ecology Research

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

Bacterial diversity and antibiotic resistances of abundant aerobic culturable bacteria in input and output samples of fifteen German biogas plants – Thorsten Schauss – Journal of Applied Microbiology

Food microbiology

The Core and Seasonal Microbiota of Raw Bovine Milk in Tanker Trucks and the Impact of Transfer to a Milk Processing Facility – Mary E. Kable – mBio

Water and extremophile microbiome

Microbial community diversity and composition varies with habitat characteristics and biofilm function in macrophyte-rich streams – Peter S. Levi – Oikos

Evaluation of Alternative High-Throughput Sequencing Methodologies for the Monitoring of Marine Picoplanktonic Biodiversity Based on rRNA Gene Amplicons – Isabel Ferrera- Frontiers in Marine Science

Book Chapter: Bacteria, Archaea and Viruses of Soda Lakes – William D. Grant – Soda Lakes of East Africa

Bioinformatics and metagenomics

ResistoMap – online visualization of human gut microbiota antibiotic resistome – Konstantin Yarygin – bioRxiv

Techniques

Protocols.io: Virtual Communities for Protocol Development and Discussion – Leonid Teytelman – PLOS Biology

More microbiology

The Ecology and Evolution of Microbial Competition – Melanie Ghoul – Trends in Microbiology

Microbes in the news

How Designers and Scientists Are Using Bees to Map NYC’s Microbes – Liz Stinson – Wired

Graphic novel about World War I depicts gross realities of dysentery – Carolyn Webb – The Age Victoria

The newest food trend: fermentation – Ted Weesner – Boston Globe

 

 

August 23, 2016

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The bagpipe microbiome, antibiotic disturbance and diabetes risk, tubeworm metamorphosis, and immune tolerance to intestinal bacteria.

Jobs

Assistant or Associate Professor in Immunology (Tenure Track), Division of Immunology of the Department of Microbiology & Immunobiology at Harvard Medical School, Boston, MA

Assistant/Associate/Professor of Microbiology and Infectious Disease, Lincoln Memorial University, Harrogate, TN

Respiratory microbiome

Bagpipe lung; a new type of interstitial lung disease? – Jenny King – Thorax

Human gut microbiome / bioinformatics

Bioinformatics support for the Tübiom community gut microbiome project – Sina Beier- PeerJ Preprint

Review: Eosinophils, probiotics, and the microbiome – Helene F. Rosenberg – Journal of Leukocyte Biology

Animal experiments

Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice – Alexandra E. Livanos – Nature Microbiology

Antibiotic Therapy During Infancy Increases Type 1 Diabetes Risk in Mice – Alison F. Takemura – The Scientist

Life Inside an Acorn: How Microclimate and Microbes Influence Nest Organization in Temnothorax Ants – Joseph Karlik – Ethology

Stepwise metamorphosis of the tubeworm Hydroides elegans is mediated by a bacterial inducer and MAPK signaling – Nicholas J. Shikuma – PNAS

Strange experiment: Gut microbiota can transfer fiber characteristics and lipid metabolic profiles of skeletal muscle from pigs to germ-free mice – Honglin Yan – Scientific Reports

pH drop impacts differentially skin and gut microbiota of the Amazonian fish tambaqui (Colossoma macropomum) – François-Étienne Sylvain – Scientific Reports

Immune tolerance to an intestine-adapted bacteria, Chryseobacterium sp., injected into the hemocoel of Protaetia brevitarsis seulensis – Jiae Lee – Scientific Reports

Alternative for antibiotics: Predatory bacteria are nontoxic to the rabbit ocular surface – Eric G. Romanowski – Scientific Reports

Animal microbiome

Multi-marker metabarcoding of coral skeletons reveals a rich microbiome and diverse evolutionary origins of endolithic algae – Vanessa Rossetto Marcelino – Scientific Reports

Techniques
Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data – Ran Blekhman – Scientific Reports

Microbes in the news

Why We Sit on One Type of Stool but, Ideally, Not on Another – Julie Taylor – uBiome Blog
Gene-modified soil bacteria promise eco-friendly computing. The US Navy is creating nanowires from one of the most renewable resources on the planet – Jon Fingas – EnGadget

Inaugural ACS Infectious Diseases Young Investigator Awards Winners Announced: Audrey Odom, Timothy Wencewicz, Marcos Pires – ACS Axial

Ghent scientist uses bacteria to remove methane from air – Andy Furniere – Flanders Today

Microbes are More Social Than You Think, But Not Always in a Good Way – Jeffrey Marlow – Discover

Science, publishing, and career

More Faculty Diversity, Not on Tenure Track – Colleen Flaherty – InsideHigherEd

 

the Macroscope – a Big Picture view of Planet Earth… articles, essays, and photographs by Jonathan Foley

August 9, 2016

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Climate change and increasing Vibrio species in North Atlantic, microbiome of the aging mouth, Antarctic soil around Little Auk colony.

Events

5th Exploring Human Host-Microbiome Interactions in Health and Disease – Welcome Genome Campus, Cambridge, UK, 7-9 September 2016

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

Hot topics in microbiology: Campden BRI conference – Campden BRI, Chipping Campden, Gloucestershire, UK, October 13-14

Today & tomorrow – live webcast – Standards for Microbiome Measurements @NIST – Jonathan Eisen – MicroBEnet

General microbiome

Note: includes 16S rRNA gene studies as well, so not metagenomic sensu stricto: An overview of major metagenomic studies on human microbiomes in health and disease – Hongfei Cui – Quantitative Biology

Brazil: A Step Forward to Empower Global Microbiome Research Through Local Leadership – Victor S. Pylro – Trends in Microbiology

Human oral microbiome

Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms – Takahiko Shiba – Scientific Reports

Oral microbial community typing of caries and pigment in primary dentition – Yanhui Li – BMC Genomics

Review: The subgingival periodontal microbiota of the aging mouth – Magda Feres – Periodonotology 2000

Human respiratory microbiome

Review: The microbiome in chronic inflammatory airway disease: A threatened species – Robin John Green – The South African Medical Journal

Review: Lung microbiome in human immunodeficiency virus infection – Homer L. Twigg IIIa – Translational Research

Human vaginal microbiome

Evaluation of the vaginal flora in pregnant women receiving opioid maintenance therapy: a matched case-control study – Alex Farr – BMC Pregnancy Childbirth

Human gut microbiome

Microbial Factors Associated with Postoperative Crohn’s Disease Recurrence – Emily K. Wright – Journal of Crohn’s and Colitis

The mucosal microbiota in a young child with severe non-Helicobacter gastritis – Geoffrey A. Preidis – Therapeutic Advances in Gastroenterology

Profile of Gut Microbiota Associated With the Presence of Hepatocellular Cancer in Patients With Liver Cirrhosis – M. Grąt – Transplantation Proceedings

Comparison of the gut microbial community between obese and lean peoples using 16S gene sequencing in a Japanese population – Akira Andoh – Journal of Clinical Biochemistry and Nutrition

Book Chapter: The Second Brain and Possible Interactions with the Heart – Rosa Sollazzo – Psychotherapy for Ischemic Heart Disease

Infection microbiology

Comparison of methods for the identification of microorganisms isolated from blood cultures – Aydir Cecília Marinho Monteiro – Annals of Clinical Microbiology and Antimicrobials

Animal experiments

Disturbance in the Mucosa-Associated Commensal Bacteria Is Associated with the Exacerbation of Chronic Colitis by Repeated Psychological Stress; Is That the New Target of Probiotics? – Sohei Arase – PLOS ONE

Role of the Gut Microbiome in Modulating Arthritis Progression in Mice – Xiaofei Liu – Scientific Reports

Salmonella Typhimurium utilizes a T6SS-mediated antibacterial weapon to establish in the host gut – Thibault G. Sana – PNAS

Animal microbiome

Does adaptive radiation of a host lineage promote ecological diversity of its bacterial communities? A test using gut microbiota of Anolis lizards – Tiantian Ren – Molecular Ecology

The gut microbiota of the pine weevil is similar across Europe and resembles that of other conifer-feeding beetles – Aileen Berasategui – Molecular Ecology

Plant, root, and soil microbiome

The Arctic soil bacterial communities in the vicinity of a little auk colony – Sylwia Zielinska – Frontiers in Microbiology

Soil Fungal:Bacterial Ratios Are Linked to Altered Carbon Cycling – Ashish A. Malik – Frontiers in Microbiology

Ancient landscapes and the relationship with microbial nitrification – Sasha N. Jenkins – Scientific Reports

Long-term antibiotic exposure in soil is associated with changes in microbial community structure and prevalence of class 1 integrons – David W. Cleary – FEMS Microbiology Ecology

Are Epiphytic Microbial Communities in the Carposphere of Ripening Grape Clusters (Vitis vinifera L.) Different between Conventional, Organic, and Biodynamic Grapes? – Elizabeth Kecskeméti – PLOS ONE

Bacterial communities in Antarctic lichens – Chae Haeng Park – Antarctic Science

Water and extremophile microbiome

Climate influence on Vibrio and associated human diseases during the past half-century in the coastal North Atlantic – Luigi Vezzulli – PNAS

Press: We’re trashing the oceans — and they’re returning the favor by making us sick – Chris Mooney – The Washington Post
Deadly Bacteria Spread across Oceans as Water Temperatures Rise. Cholera bacteria and others arise in more places and in greater abundance – Umair Irfan – Scientific American
Warming seas linked to rise in cholera bacteria in Europe and US – Brian Owens – New Scientist

Microbial community structure in hypolentic zones of a brine lake in a desert plateau, China – Wenzhen Yuan – Environmental Earth Sciences

Microbial diversity in sediment ecosystems (evaporites domes, microbial mats and crusts) of hypersaline Laguna Tebenquiche, Salar de Atacama, Chile – Ana B. Fernandez – Frontiers in Microbiology

Bioreactor microbiome

The full-scale anaerobic digestion microbiome is represented by specific marker populations – Jo De Vrieze – Water Research

Viruses and phages

Challenges in the analysis of viral metagenomes – Rebecca Rose – Virus Evolution

Metagenomics and bioinformatics

Bipartite graph analyses reveal inter-domain LGT involving ultrasmall prokaryotes and their divergent, membrane-related proteins – Alexander L. Jaffe – Environmental Microbiology

FARAO – The Flexible All-Round Annotation Organizer – Rickard Hammarén – Bioinformatics

Identifying wrong assemblies in de novo short read primary sequence assembly contigs – Vandna Chawla – Journal of Biosciences

A Bayesian Framework for the Classification of Microbial Gene Activity States – Craig Disselkoen – Frontiers in Microbiology

Techniques

Evaluation of 16S rRNA gene primer pairs for monitoring microbial community structures showed high reproducibility within and low comparability between datasets generated with multiple archaeal and bacterial primer pairs – Martin A. Fischer – Frontiers in Microbiology

More microbiology

Editorial: New insights into microbial ecology through subtle nucleotide variation – A M. Eren – Frontiers in Microbiology

Neisseria meningitides Can Survive in Corpses for At Least Eleven Days – Antonio Osculati – Frontiers in Cellular and Infection Microbiology

Microbes in the news

List of papers about bias in microbiome techniques: The unbearable madness of microbiome – Mick Watson – Opiniomics

Book Review: Follow your gut – The Enormous Impact of Tiny Microbes – Daniel K. Morais – Frontiers in Microbiology

Brito went to Fiji to study mobile genes in human microbiome – Tom Fleischman – Cornell Chronicle

MSU graduate awarded NSF fellowship to study disease affecting world’s citrus crops – Denise Hoepfner – Montana State University

Bacteria Could Aid Search for Creatures On Other Planets – Elizabeth Howell – Astrobiology Magazine

U.Va. scientists make important discovery about dangerous bacteria strains
Researchers pinpoint mechanisms of C. difficile strains – Daisy Xu – Cavalier Daily

Did farming practices in China create an antibiotic resistant bacteria that’s spreading around the world? – Alanna Shaikh – United Nations Dispatch

Science, publishing, and career

Dog eat dog: is a troubled expedition to Kenya causing the Smithsonian to devour its young?
A star scientist stands accused of misconduct, but colleagues say he’s being railroaded
– Michael Balter – The Verge

A “Scientific Diversity” Intervention to Reduce Gender Bias in a Sample of Life Scientists – Corinne A. Moss-Racusin – CBE Life Sciences Education

Bik’s non-microbiology Picks

Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children – Michelle M. Stein – New England Journal of Medicine

August 5, 2016

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Urinary tract microbiome, preterm gut microbiota and humanized mice, fungi of Crocus (Saffron plant), and bead-beating artefacts.

General microbiome

Introduction to special issue of Molecular Metabolism: Microbiota: ‘bugging’ insights into metabolic regulation – Thomas Schwarz-Romond – Molecular Metabolism

Human oral microbiome

Transcriptome Analysis of B Cell Immune Functions in Periodontitis: Mucosal Tissue Responses to the Oral Microbiome in Aging – Jeffrey L. Ebersole – Frontiers in Immunology

Human respiratory microbiome

Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung – Leopoldo N Segal – Thorax

Review: Microbiome in the pathogenesis of cystic fibrosis and lung transplant-related disease – Sushma K. Cribbs – Translational Research

Human urinary tract microbiome

Evaluation of the Urinary Microbiota of Women With Uncomplicated Stress Urinary Incontinence – Krystal J. Thomas-White – American Journal of Obstetrics and Gynecology

Human gut microbiome

Review: Microbiota as Mediator of Cancer Progression and Therapy – Jilian L. Pope – Translational Research

Review: The human microbiome in rheumatic autoimmune diseases: A comprehensive review – Patrick Coit – Clinical Immunology

Review: Human gut microbiota plays a role in the metabolism of drugs – Lenka Jourova – Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub

Animal experiments

Preterm infant gut microbiota affects intestinal epithelial development in a humanized gnotobiotic mouse model – Yueyue Yu – American Journal of Physiology – Gastrointestinal and Liver Physiology

Symbiotic gut commensal bacteria act as host cathepsin S activity regulators – Alex Steimle – Journal of Autoimmunity

Research Highlight (but very harsh title): Gut microbiota: Microbiota and behaviour: visiting the sins of the mother – Paul Forsythe – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): A basis for comparative gut microbial research – Karina Gajardo – Scientific Reports

Plant, root, and soil microbiome

Molecular phylogeny, diversity, community structure and plant growth promoting properties of fungal endophytes associated with the corms of Saffron plant: an insight into the microbiome of Crocus sativus Linn – Zahoor Ahmed Wani – Fungal Biology

Leaf Treatments with a Protein-Based Resistance Inducer Partially Modify Phyllosphere Microbial Communities of Grapevine – Martina Cappelletti – Frontiers in Plant Science

The Resilience of Microbial Community under Drying and Rewetting Cycles of Three Forest Soils – Xue Zhou – Frontiers in Microbiology

Fungus-associated bacteriome in charge of their host behavior – Kristin Schulz-Bohm – Fungal Genetics and Biology

Microbiota Characterization of Compost Using Omics Approaches Opens New Perspectives for Phytophthora Root Rot Control – Josefa Blaya – PLOS ONE

Water and extremophile microbiome

Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris – Sonja Oberbeckmann – PLOS ONE

Microbial Community Responses to Increased Water and Organic Matter in the Arid Soils of the McMurdo Dry Valleys, Antarctica – Heather N. Buelow – Frontiers in Microbiology

Microbial community structure shifts are associated with temperature, dispersants and nutrients in crude oil-contaminated seawaters – Long Meng – Marine Pollution Bulletin

Bioinformatics and metagenomics

Rapid resistome mapping using nanopore sequencing – Eric van der Helm – bioRxiv

Metabolomics

Metabolomics evaluation of the impact of smokeless tobacco exposure on the oral bacterium Capnocytophaga sputigena – Jinchun Sun – Toxicology in Vitro

Training in metabolomics research. II. Processing and statistical analysis of metabolomics data, metabolite identification, pathway analysis, applications of metabolomics and its future – S. Barnes – Journal of Mass Spectrometry

Techniques

Bead-beating artefacts in the Bacteroidetes to Firmicutes ratio of the human stool metagenome – Heidi C. Vebø – Journal of Microbiological Methods

Pipeline for amplifying and analyzing amplicons of the V1–V3 region of the 16S rRNA gene – Heather K. Allen – BMC Research Notes

A Single-Batch Fermentation System to Simulate Human Colonic Microbiota for High-Throughput Evaluation of Prebiotics – Risa Takagi – PLOS ONE

More microbiology

Metabolic engineering of microbial competitive advantage for industrial fermentation processes – A. Joe Shaw – Science

Microbes in the news

AGA establishes NIH-funded registry to track fecal microbiota transplants – EurekAlert

Maternal microbial inheritance—benefits of breastfeeding – Md Zohorul Islam

ASM Agar Art Calendar 2016/2017

Science, publishing, and career

What Is the Key Best Practice for Collaborating with a Computational Biologist? – Cell Systems

University of Waterloo boosts salaries of female faculty after discrepancy found – Paola Loriggio – CP24

Bik’s Non-Microbiology Picks

Circadian regulation of sunflower heliotropism, floral orientation, and pollinator visits – Hagop S. Atamian – Science
How do sunflowers follow the Sun—and to what end? – Winslow R. Briggs – Science

August 4, 2016

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Human breast tissue microbes, foliar bacteria, SAR11 genomes, and a new book about babies growing up too clean.

Human oral microbiome

Oral, Intestinal, and Skin Bacteria in Ventral Hernia Mesh Implants – Odd Langbach – Journal of Oral Microbiology

A novel compound to maintain a healthy oral plaque ecology in vitro – Marleen M. Janus
– Journal of Oral Microbiology

Paper on periodontal disease by computer scientists, but no dentists involved, and no mentioning of ethics approval or informed consent…
Metagenomic Analysis and Features Selection in Human Oral Microbiota Associated with Periodontal Disease – Wen-Pei Chen – The 33rd Workshop on Combinatorial Mathematics and Computation Theory

Human skin/breast tissue microbiology

The Microbiome of Aseptically Collected Human Breast Tissue in Benign and Malignant Disease – Tina J. Hieken – Scientific Reports

Press: Researchers identify breast microbiome/bacterial differences between healthy and cancerous tissue – Medical Xpress

Also contains animal experiments: Transplantation of human skin microbiota in models of atopic dermatitis – Ian A. Myles – JCI Insight

Human gut microbiome

Effects of scFOS on the composition of fecal microbiota and anxiety in patients with irritable bowel syndrome: a randomized, double blind, placebo controlled study – F. Azpiroz – Neurogastroenterology & Motility

Letter: Dyspepsia and the microbiome: time to focus on the small intestine – Laurie Zhong – Gut

Review: Exposure to inorganic arsenic can lead to gut microbe perturbations and hepatocellular carcinoma – Jonathan Choiniere – Acta Pharmaceutica Sinica B

Review: Modulation of type 1 and type 2 diabetes risk by the intestinal microbiome –
Alexandra Paun – Pediatric Diabetes

Animal experiments

Pterostilbene-induced changes in gut microbiota composition in relation to obesity – Usune Etxeberria – Molecular Nutrition & Food Research

The skin microbiome in allergen-induced canine atopic dermatitis – Felipe Pierezan – Veterinary Dermatology

Plant, root, and soil microbiome

Foliar bacteria and soil fertility mediate seedling performance: a new and cryptic dimension of niche differentiation – Eric A. Griffin – Ecology

DGGE: Effect of karst rocky desertification on soil fungal communities in Southwest China – P.C. Wang – Genetics and Molecular Research

Water and extremophile microbiome

SAR11 bacteria linked to ocean anoxia and nitrogen loss – Despina Tsementzi – Nature

Press: Global warming, a dead zone and surprising bacteria – Phys.org

Sulfate reduction and inorganic carbon assimilation in acidic thermal springs of the Kamchatka peninsula – E. N. Frolov – Microbiology

Book Chapter: Bacterial Diversity of the Boka Kotorska Bay – Sandra Jokanović – The Handbook of Environmental Chemistry

Bioinformatics and metagenomics

An integrated metagenomics pipeline for strain profiling reveals novel patterns of transmission and global biogeography of bacteria – Stephen Nayfach – bioRxiv

Advances in the recovery of haplotypes from the metagenome – Samuel M Nicholls – bioRxiv

Techniques

Virtual microfluidics for digital quantification and single-cell sequencing – Liyi Xu – Nature Methods

Microbial Nanoculture as an Artificial Microniche – Tagbo H. R. Niepa – Scientific Reports

Considerations for optimizing microbiome analysis using a marker gene – Jacobo de la Cuesta-Zuluaga – Frontiers in Nutrition

Microbes in the news

Dirty baby: Just how clean does your child need to be? – Bill Daley – Chicago Tribune

New book: Let Them Eat Dirt. Saving Your Child From an Oversanitized World – B. Brett Finlay and Marie-Claire Arrieta

Cloud computing used to analyze microbiological samples – Tim Sandle – Digital Journal

Bacteria Show Capacity for Rapid, Beneficial Mutations – University of Texas News

Video: Vibrio cholerae swimming in the gut of a live zebrafish – Phys.org

How the microbiome will lead a revolution in the consumerization of personalized medicine and diet – Kobi Gershoni – Tech Crunch
Science, publishing, and career

Scholarly Olympics: How the games have shaped research. A graphical guide to the impact of the Olympics on science – Ramin Skibba – Nature

‘Kudos’ promises to help scientists promote their papers to new audiences
Increasingly popular social-media tool says it can maximize reach and impact of research – Jeffrey Perkel – Nature

August 1, 2016

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Storage conditions of infant fecal microbiota, microbial pinnacles, bioaerosols in chicken production facilities.

General microbiome

Special issue of Microbial Biotechnology, including:
Biome engineering-2020 – Harald Brüssow
Microbial bioinformatics 2020 – Mark J. Pallen
Next-generation studies of microbial biofilm communities – Scott A. Rice
Plant–microbe partnerships in 2020 – Birgit Mitter

Opinion: Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human Gut – Eveline Adam – Frontiers in Microbiology

Pregnancy and birth

Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room? – Alexander G Shaw – Microbiome

Gut Microbiota Richness and Composition and Dietary Intake of Overweight Pregnant Women Are Related to Serum Zonulin Concentration, a Marker for Intestinal Permeability – Kati Mokkala – The Journal of Nutrition

Review: Microbial Changes during Pregnancy, Birth, and Infancy – Meital Nuriel-Ohayon – Frontiers in Microbiology

Human eye microbiome

Ocular surface microbiome in meibomian gland dysfunction in Auckland, New Zealand –
Grant A. Watters – Clinical & Experimental Ophtalmology

Human gut microbiome

Microbial diversity in individuals and their household contacts following typical antibiotic courses – Shira R. Abeles – Microbiome

Microbial Factors Associated with Post-Operative Crohn’s Disease Recurrence – Emily K Wright – Journal of Crohn’s and Colitis

Efficacy of antineoplastic treatment is associated with the use of antibiotics that modulate intestinal microbiota – Natali Pflug – OncoImmunology

Review: The oesophageal microbiome: an unexplored link in obesity-associated oesophageal adenocarcinoma – Nadeem O. Kaakoush – FEMS Microbiology Ecology

Review: Normal, Regular and Standard: Scaling the Body through Fecal Microbial Transplants – Matthew J. Wolf-Meyer – Medical Anthropology Quarterly

Review: Gut Microbiota Imbalance and Base Excision Repair Dynamics in Colon Cancer – Debolina Ray – Journal of Cancer

Review: Fine-Tuning Cancer Immunotherapy: Optimizing the Gut Microbiome – Jonathan M. Pitt – Cancer Research

Review: Irritable bowel syndrome, the microbiota and the gut-brain axis – Hans Raskov – Gut Microbes

Animal microbiome

Fish: Alterations of the gut microbiome of largemouth bronze gudgeon (Coreius guichenoti) suffering from furunculosis – Tongtong Li – Scientific Reports

Plant, root, and soil microbiome

Structure of bacterial communities in soil following cover crop and organic fertilizer incorporation – Adria L. Fernandez – Applied Microbiology and Biotechnology

Correlation analysis of enzyme activities and deconstruction of ammonia-pretreated switchgrass by bacterial-fungal communities – Abhiney Jain – Bioresource Technology

Variations of rhizosphere bacterial communities in tea (Camellia sinensis L.) continuous cropping soil by high-throughput pyrosequencing approach – Y.C. Li – Journal of Applied Microbiology

High culturability of epiphytic bacteria and frequency of biosurfactant producers on leaves – Adrien Y. Burch – Applied and Environmental Microbiology

Desiccation of sediments affects assimilate transport within aquatic plants and carbon transfer to microorganisms – Isabell von Rein – Plant Biology

Review: Emergence of plant and rhizospheric microbiota as stable interactomes – Prasun Bandyopadhyay – Protoplasma

Water and extremophile microbiome

Growth of elaborate microbial pinnacles in Lake Vanda, Antarctica – D. Y. Sumner – Geobiology

Diversity and succession of autotrophic microbial community in high-elevation soils along deglaciation chronosequence – Jinbo Liu – FEMS Microbial Ecology

Air microbiome

High throughput genomic sequencing of bioaerosols in broiler chicken production facilities – Kate M. O’Brien – Microbial Biotechnology

Bioinformatics

RevEcoR: an R package for the reverse ecology analysis of microbiomes – Yang Cao – BMC Bioinformatics

Metabolomics

Review: Metabolites: messengers between the microbiota and the immune system – Maayan Levy – Genes & Development

Techniques

Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering – Geoffrey L. House – Applied and Environmental Microbiology

Microbes in the news
Why is microbiome so important? Gut instinct tells you – Jessica le Roux – FoodMed

Science, publishing, and career

Intentional equity – France A. Córdova – Science

Lost in Translation: From scientists to the press and to the public – The Microbial Menagerie

July 29, 2016

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Bifidobacteria/Spirochaetes trade-off in Italians vs. Hadza, asthma, transferring depression with human stool to rats, sea squirts symbionts, spacial structure of biofilms, and a glowing review of Ed Yong’s book “I Contain Multitudes”.

General microbiome

Dysbiosis Across Multiple Body Sites in Critically Ill Adult Surgical Patients – Andrew Yeh – Shock

Pregnancy / human oral microbiome

Smoking, pregnancy and the subgingival microbiome – Akshay D. Paropkari – Scientific Reports

Review: An Integrated Review of Intestinal Microbiota in the Very Premature Infant – Melissa C. Dollings –  Neonatal Network

Human respiratory microbiome

Bacterial microbiota of the upper respiratory tract and childhood asthma – Martin Depner – Journal of Allergy and Clinical Immunology

Review: The role of anaerobic bacteria in the cystic fibrosis airway – Laura J. Sherrard – Current Opinion in Pulmonary Medicine

Human vaginal microbiome

Commentary: The relationship between the vaginal microbiome and human health – MR Millar – BJOG

Human gut microbiome

Variations in the Post-weaning Human Gut Metagenome Profile As Result of Bifidobacterium Acquisition in the Western Microbiome – Matteo Soverini – Frontiers in Microbiology

Pediatric obesity is associated with an altered gut microbiota and discordant shifts in Firmicutes populations – Alessandra Riva – Environmental Microbiology

Histamine-secreting microbes are increased in the gut of adult asthma patients – Weronika Barcik – Journal of Allergy and Clinical Immunology

Dietary Supplementation with Rice Bran or Navy Bean Alters Gut Bacterial Metabolism in Colorectal Cancer Survivors – Amy M. Sheflin – Molecular Nutrition & Food Research

Four-week consumption of a Bifidobacterium bifidum strain modulates dominant intestinal bacterial taxa and fecal butyrate in healthy adults – Giorgio Gargari – Applied and Environmental Microbiology

Fecal microbiota transplantation for patients with steroid-resistant/dependent acute graft-versus-host disease of the gut – Kazuhiko Kakihana – Blood

Trial: Effect of prebiotic intake on gut microbiota, intestinal permeability and glycemic control in children with type 1 diabetes: study protocol for a randomized controlled trial – Josephine Ho – Trials

Opinion: How stable is the human gut microbiota? And why this question matters – Harald Brüssow – Environmental Microbiology

Research highlight: Microbial mobilomes differ between societies – Naomi Attar – Nature Reviews Microbiology

Review: High-Resolution Characterization of the Human Microbiome – Cecilia Noecker – Translational Research

Review: Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases – Mingming Sun – Journal of Gastroenterology

Review: The influence of gut derived CD39 regulatory T cells in CNS demyelinating disease – Javier Ochoa-Repáraz – Translational Research

Review: Fecal microbiota transplantation in inflammatory bowel disease: the quest for the holy grail – B Pigneur – Mucosal Immunology

Review: The Gut Microbiota in Immune-Mediated Inflammatory Diseases – Jessica D. Forbes – Frontiers in Microbiology

Review: Regulation of Autoimmunity by the Microbiome – Carlos R. Zárate-Bladés – DNA and Cell Biology

Animal experiments

Transferring the blues: Depression-associated gut microbiota induces neurobehavioural changes in the rat – John R. Kelly – Journal of Psychiatric Research

The microbiota contributes to CD8+ T cell activation and nutrient malabsorption following intestinal infection with Giardia – Infection and Immunity – Aleksander Keselman

Gut Microbial Membership Modulates CD4 T Cell Reconstitution and Function after Sepsis – Javier Cabrera-Perez – Journal of Immunology

Metabolite exchange within the microbiome produces compounds that influence Drosophila behavior – Caleb N. Fischer – bioRxiv

Variation in the Gut Microbiota of Termites (Tsaitermes ampliceps) Against Different Diets – Lijuan Su – Applied Biochemistry and Biotechnology

Animal microbiome

Endozoicomonas Are Specific, Facultative Symbionts of Sea Squirts – Lars Schreiber – Frontiers in Microbiology

Comparison of a modified phenol/chloroform and commercial-kit methods for extracting DNA from horse fecal material – Ali H.D. Janab -Journal of Microbiological Methods

Death Becomes Them: Bacterial community dynamics and stilbene antibiotic production in Galleria mellonella cadavers killed by Heterorhabditis/Photorhabdus – Amanda C. Wollenberg – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium – German Zafra – Journal of Hazardous Materials

Water and extremophile microbiome

Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale – Amit Vikram – Microbial Ecology

Characterizing microbial diversity in production water from an Alaskan mesothermic petroleum reservoir with two independent molecular methods – Vinh D. Pham – Environmental Microbiology

Protocol: Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME – Matthieu Leray – Marine Genomics

Protocol: Sampling of Riverine or Marine Bacterial Communities in Remote Locations: From Field to Publication – Katja Lehmann – Marine Genomics

Microbes in space

Assessment of the Forward Contamination Risk of Mars by Clean Room Isolates from Space-Craft Assembly Facilities through Aeolian Transport – a Model Study – Luc van Heereveld – Origins of Life and Evolution of Biospheres

Built environment microbiome

Figures appear to show a gradual change, not a break, but: Summer holidays as break-point in shaping a tannery sludge microbial community around a stable core microbiota – Cesira Giordano – Scientific Reports

Food microbiology

Detailed analyses of the bacterial populations in processed cocoa beans of different geographic origin, subject to varied fermentation conditions – Cristian Bortolini – International Journal of Food Microbiology

Bioinformatics and metagenomics

A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets – Scott C. Ritchie – Cell Systems

Techniques

The effect of DNA extraction methodology on gut microbiota research applications – Konstantinos Gerasimidis – BMC Research Notes

Biofilms

Review: Spatial structure, cooperation and competition in biofilms – Carey D. Nadell – Nature Reviews Microbiology

Microbes in the news

A glowing book review: Living in a microbial world, book review of “I Contain Multitudes The Microbes Within Us and a Grander View of Life” by Ed Yong – Susan Perkins – Science

State College of Florida, New College graduate wins microbiology award: Stephanie Morgan’s research won an award at the Small World Initiative Symposium – Bradenton Herald

Microbiology: A budding researcher creates a stir with her LIST-supported project: Camilla Hurst – Luxembourg Institute of Science And Technology (LIST)

‘Bugs’ on the subway: Monitoring the microbial environment to improve public health – Harvard

‘Nose-y’ Bacteria Could Yield A New Way To Fight Infection – Carolyn Beans – NPR

The Marine Microbiome – A treasure trove of scientific and industrial potential – Cordis Europa
Video: Revealing the Secrets of Marine Microbes: methods that are being used to isolate and culture marine microorganisms – MaCuMBA project

July 26, 2016

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The last common ancestor, pika gut microbiome, fire-fighting chemicals and soil microbiome, improved Illumina-compatible 18S rRNA primers.

Jobs

Verily (Google-associated) is looking for a Microbiome Research Associate

Pregnancy and birth

Probiotic properties of lactic acid bacteria isolated from human milk – N.A. Reis – Journal of Applied Microbiology

Human oral microbiome

High Throughput Quantitative Method for Assessing Coaggregation among Oral Bacterial Species – Elizabeth Levin-Sparenberg – Letters in Applied Microbiology

Periodontal infectogenomics: systematic review of associations between host genetic variants and subgingival microbial detection – Luigi Nibali – Journal of Clinical Periodontology

Human respiratory microbiome

Upper airway viruses and bacteria and clinical outcomes in children with cough – Kerry-Ann F. O’Grady – Pediatric Pulmonology

Human skin microbiome

Hypothesis: The skin microbiome: Is it affected by UV-induced immune suppression? – Vijaykumar Patra – Frontiers in Microbiology

Human gut microbiome

Gut microbiota-host interactions and juvenile idiopathic arthritis – Miika Arvonen – Pediatric Rheumatology

Designing fecal microbiota transplant trials that account for differences in donor stool efficacy – Scott W. Olesen – bioRxiv

Probiotics and the Microbiome in Celiac Disease: A Randomised Controlled Trial – Joanna Harnett – Evidence-Based Complementary and Alternative Medicine

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

Human vaginal microbiome

More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria – Sujatha Srinivasan – The Journal of Infectious Diseases

The Effects of Hormones and Vaginal Microflora on the Glycome of the Female Genital Tract: Cervical-Vaginal Fluid – Bernard J. Moncla – PLOS ONE

Review: New Systems for Studying Intercellular Interactions in Bacterial Vaginosis – Melissa M. Herbst-Kralovetz – The Journal of Infectious Diseases

Animal experiments

Lactulose differently modulates the composition of luminal and mucosal microbiota in C57BL/6J mice – Bingyong Mao – Journal of Agricultural and Food Chemistry

American Ginseng Attenuates Colitis Associated Colon Carcinogenesis in Mice: Impact on Gut Microbiota and Metabolomics – Chong-Zhi Wang – Cancer Prevention Research

Alterations of Gut Microbiota After Roux-en-Y Gastric Bypass and Sleeve Gastrectomy in Sprague-Dawley Rats – Yikai Shao – Obesity Surgery

Animal microbiome

Diet diversity is associated with beta but not alpha diversity of pika gut microbiota – Huan Li – Frontiers in Mcrobiology

The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats – Alejandra Hernandez-Agreda – mBio

Perspective: Hominid superorganisms – Julia A. Segre – Science

Plant, root, and soil microbiome

Long-term response of soil microbial communities to fire and fire-fighting chemicals –
A. Barreiro – Biology and Fertility of Soils

Desert Perennial Shrubs Shape the Microbial-Community Miscellany in Laimosphere and Phyllosphere Space – Varsik Martirosyan – Microbial Ecology

Lichen-associated Fungal Community in Hypogymnia hypotrypa (Parmeliaceae, Ascomycota) Affected by Geographic Distribution and Altitude – Yanyan Wang – Frontiers in Microbiology

Water management impacts rice methylmercury and the soil microbiome – Sarah E. Rothenberg – Science of the Total Environment

Ecological restoration of a copper polluted vineyard: Long-term impact of farmland abandonment on soil bio-chemical properties and microbial communities – Luciano Cavani – Journal of Environmental Management

Review: Soil C and N models that integrate microbial diversity – Benjamin P. Louis – Environmental Chemistry Letters

Water and extremophile microbiome

Genomes of Abundant and Widespread Viruses from the Deep Ocean – Carolina Megumi Mizuno – mBio

Microbial communities associated with Antarctic snow pack and their biogeochemical implications – Runa Antony – Microbiological Research

Novel chytrid lineages dominate fungal sequences in diverse marine and freshwater habitats – André M. Comeau – Scientific Reports

Metabolomics

Review: Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health – Pamela Vernocchi – Frontiers in Microbiology

Functional foods

Review: Fermented Foods: Are They Tasty Medicines for Helicobacter pylori Associated Peptic Ulcer and Gastric Cancer? – Mydhily R. B. Nair – Frontiers in Microbiology

Bioinformatics

A novel alignment-free method for detection of lateral genetic transfer based on TF-IDF – Yingnan Cong – Scientific Reports
Exploring lateral genetic transfer among microbial genomes using TF-IDF – Yingnan Cong – Scientific Reports

Techniques

Design and Evaluation of Illumina MiSeq Compatible Primers for the 18S rRNA Gene for Improved Characterization of Mixed Microalgal Communities – Ian M. Bradley – Applied and Environmental Microbiology

More microbiology

Are multi-omics enough? – Cristina Vilanova – Nature Microbiology

Review: Bacterial Communities: Interactions to Scale – Reed M. Stubbendieck – Frontiers in Microbiology

The physiology and habitat of the last universal common ancestor – Madeline C. Weiss – Nature Microbiology

Press: Scientists find Luca, a single-cell, bacterium-like organism that is the common ancestor of all life on Earth – Andrew Griffin – Independent
Behold LUCA, the Last Universal Common Ancestor of Life on Earth – Jason Daley – Smithsonian
Our last common ancestor inhaled hydrogen from underwater volcanoes – Robert F. Service – Science
Meet Luca, the Ancestor of All Living Things – Nicholas Wade – New York Times

Microbes in the news

What your gut microbiome may be telling you – Katrina Clarke – The Record

Healthy microbiome supports antibiotic-free production – World Poultry

Charlottesville Lab to Test Microbiology of Local Breweries – NBC29

Nanostructured bacterial film makes new mortar resistant to water uptake – NanoWerk

Bik’s non-microbiology Picks

The Dutchies are still holding the top positions! A century of trends in adult human height – NCD Risk Factor Collaboration (NCD-RisC) – eLIFE