Category Archives: Human respiratory

July 2, 2016

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Colonic transit time, innovations in artificial gut systems, and how the majority of the human gut microbiome members can be cultured.

Human respiratory microbiome

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis – Clark A. Santee – Microbiome

Metagenomics Study of Viral Pathogens in Undiagnosed Respiratory Specimens
and Identification of Human Enteroviruses at a Thailand Hospital – Yanfei Zhou – American Journal of Tropical Medicine and Hygiene

Review: The respiratory microbiome of HIV-infected individuals – MB Lawani – Expert Review of Anti-infective Therapy

Review: A tale of two sites: how inflammation can reshape the microbiomes of the gut and lungs – Brittan S. Scales – Journal of Leukocyte Biology

Human gut microbiome

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut – Henrik M. Roager – Nature Microbiology

Behind the paper: How we got captivated by colonic transit time – Henrik Munch Roager – Nature Microbiology Community

Datafying microbes: Malnutrition at the intersection of genomics and global health – Amber Benezra – BioSocieties

Several reviews in the July issue of Therapeutic Advances in Gastroenterology:
The interplay between the microbiome and the adaptive immune response in cancer development – Edda Russo
The intestinal microbiome, barrier function, and immune system in inflammatory bowel disease: a tripartite pathophysiological circuit with implications for new therapeutic directions – Stephen M. Vindigni
Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ – Caitriona M. Guinane
Novel perspectives on therapeutic modulation of the gut microbiota – Justin L. McCarville

Review: The Brain-Body-Microbial Communities: A Crosstalk and Stress Exchange
Beyond the “Gut hypothesis” – Afifi Ma – Abnormal and Behavioural Psychology

Review: The Role of the Microbial Metabolites Including Tryptophan Catabolites and Short Chain Fatty Acids in the Pathophysiology of Immune-Inflammatory and Neuroimmune Disease – Gerwyn Morris – Molecular Neurobiology

Animal experiments

Relationship between the microbiota in different sections of the gastrointestinal tract, and the body weight of broiler chickens – Geon Goo Han – Springer Plus

The upper respiratory tract microbiome and its potential role in bovine respiratory disease and otitis media – Svetlana F. Lima – Scientific Reports

Review: Farewell to Animal Testing: Innovations on Human Intestinal Microphysiological Systems – Tae Hyun Kang – Micromachines

Plant, root, and soil microbiome

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau – Kaoping Zhang – Frontiers in Microbiology

Bacterial diversity in the rhizosphere of two phylogenetically closely related plant species across environmental gradients – Xiaofan Na – Journal of Soils and Sediments

Soil microbial communities of three major Chinese truffles in Southwest China – Yu Fu – Canadian Journal of Microbiology

Review: Ecology of nitrogen fixing, nitrifying and denitrifying microorganisms in tropical forest soils – Silvia Pajares – Frontiers in Microbiology

Water and extremophile microbiome

Metagenomic analysis of microbial community of an Amazonian geothermal spring in Peru – Sujay Paul – Genomics Data

Characterization of microbial mat microbiomes in the modern thrombolite ecosystem of Lake Clifton, Western Australia using shotgun metagenomics – John G. Warden – Frontiers in Microbiology

Built environment microbiome

Microbes in the Water Infrastructure: Underpinning Our Society – Takashi Narihiro – Microbes and Environments

Techniques / Metabolomics

Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling – Jennifer T. Lau – Genome Medicine

A Microbiome DNA Enrichment Method for Next-Generation Sequencing Sample Preparation – Erbay Yigit – Current Protocols in Molecular Biology

Sample preparation optimization in fecal metabolic profiling – Olga Deda – Journal of Chromatography B

Viruses and phages

Survival studies of a temperate and lytic bacteriophage in bovine faeces and slurry – Sepo Nyambe – Journal of Applied Microbiology

Microbes in the news

Conference report: Machine Learning Method Differentiates Between Healthy Male, Female Microbiomes: Topological Data Analysis – UC San Diego

A New Role for Marine Archaea. Researchers discover acetogenesis in archaea, suggesting an important role for these little-studied organisms in generating organic carbon below the seafloor – Catherine Offord – The Scientist

Stop worrying about GMOs; it’s that organic granola bar that could make you sick: Listeria – Henry I. Miller – LA Times

USM marine microbiologist Jay Grimes weighs in on vibrio vulnificus – WDAM

Chesterfield Royal scientists send ripples around the NHS – Andy Done-Johnson – Derbyshire Times

Efficiency in the pathology lab: Friend or Foe; the probiotic power of helminths can prevent Crohn’s Disease – Anouk Gouvras – BioMedCentral blog

Supplement may switch off cravings for high-calorie foods – Stephen Feller – UPI
Cravings for high-calorie foods may be switched off by new food supplement – Kate Wighton – Imperial College London

Science, publishing, and career

“He Thinks He’s Untouchable”: Michael Katze, famous for his studies of Ebola and the flu, ran a lab at the University of Washington where intoxication and sexual harassment went unchecked – Azeen Ghorayshi – Buzzfeed

July 1, 2016

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NIH’s Lita Proctor writes about the Human Microbiome Project, oral microbiome among Cheyenne and Arapaho, Cystic Fibrosis, responses to resistant starch, the Swan Goose, sugarcane, litter decomposition.

General microbiome

Review: The National Institutes of Health Human Microbiome Project – Lita M. Proctor – Seminars in Fetal and Neonatal Medicine

Pregnancy and birth

Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota – Rocio Martin – PLOS ONE

Human oral microbiome

Oral microbiome diversity among cheyenne and arapaho individuals from Oklahoma – Andrew T. Ozga – American Journal of Physical Anthropology

Human respiratory microbiome

Pyrosequencing Unveils Cystic Fibrosis Lung Microbiome Differences Associated with a Severe Lung Function Decline – Giovanni Bacci – PLOS ONE

Human skin microbiome

The skin microbiome is different in pediatric versus adult atopic dermatitis –
Baochen Shi – Journal of Allergy and Clinical Immunology

Just colony counts: Chlorhexidine avoids skin bacteria recolonization more than triclosan – Juan H. Macias – American Journal of Infection Control

Human gut microbiome

Variable responses of human microbiomes to dietary supplementation with resistant starch – A. Venkataraman – Microbiome

Duodenal bacteria from patients with celiac disease and healthy subjects distinctly affect gluten breakdown and immunogenicity – Alberto Caminero – Gastroenterology

Predominance of Lactobacillus spp. among patients who do not acquire multidrug-resistant organisms – Rafael Araos – Clinical Infectious Diseases

Nutrition and the Microbiome: Special Edition of the Annals of the New York Academy of Sciences
Review: Nutrition and the microbiome – Karin Moelling
Review: Nutrition meets the microbiome: micronutrients and the microbiota – Hans K. Biesalski

Letter: Microbiota and Alcoholic Liver Disease – Peng Chen – Alcoholism: Clinical and Experimental Research

Animal experiments

Sex differences and hormonal effects on gut microbiota composition in mice – Elin Org – Gut Microbes

Animal microbiome

Distinctive gut microbial community structure in both the wild and farmed Swan goose (Anser cygnoides) – Wen Wang – Journal of Basic Microbiology

The gut microbiome of the sea urchin, Lytechinus variegatus from their natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles – Joseph A. Hakim – FEMS Microbiology Ecology

Analysis of microbiota on abalone (Haliotis discus hannai) in South Korea for improved product management – Min-Jung Lee – International Journal of Food Microbiology

Bacterial endosymbionts protect aphids in the field and alter parasitoid community composition – Lukas Rothacher – Ecology
Midgut fungal and bacterial microbiota of Aedes triseriatus and Aedes japonicus shift in response to La Crosse virus infection – Ephantus J. Muturi – Molecular Ecology

Plant, root, and soil microbiome

The importance of C, N and P as driver for bacterial community structure in German beech dominated forest soils – Fabian Bergkemper – Journal of Plant Nutrition and Soil Science

Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome – Rafael Soares Correa de Souza – Scientific Reports

Life in leaf litter: novel insights into community dynamics of bacteria and fungi during litter decomposition – Witoon Purahong – Molecular Ecology

Endophytic microbial diversity of the halophyte Arthrocnemum macrostachyum across plant compartments – M. del R. Mora-Ruiz – FEMS Microbiology Ecology

Conference abstract: High diversity of enzymes in plant-associated microbiomes – Christina A. Müller – New Biotechnology

Review: Plant-Mediated Systemic Interactions Between Pathogens, Parasitic Nematodes, and Herbivores Above- and Belowground – Arjen Biere – Annual Review of Phytopathology

Unearthed! The Amazing Microbiome Exposed: Editor’s Note – Stephen L. Young – Bulletin of the Ecological Society of America
Unearthed! The Amazing Microbiome Exposed: The Arising Researcher – Marnie E. Rout
Unearthed! The Amazing Microbiome Exposed: The Established Researcher – John Klironomos

Water microbiome

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments – Benjamin J. Tully – Applied and Environmental Microbiology

Built environment microbiome

Evidence of Avian and Possum Fecal Contamination in Rainwater Tanks as Determined by Microbial Source Tracking Approaches – W. Ahmed – Applied and Environmental Microbiology

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA – Lee F. Stanish – PLOS ONE

Microbes in space

Review: Venturing into new realms? Microorganisms in space – Christine Moissl-Eichinger – FEMS Microbiology Reviews

Techniques

Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy – Aina E. F. Moen – BMC Research Notes

Microbes in the news

The North American Beaver: Castor canadensis : A look at our local Canadian friend’s microbes – Megan McGrath – Genotek’s The Microbiome Snapshot

Human Microbiome Market : Growth, Development, and Outlook 2014 – 2020 – SB Wire

uBiome Completely Re-Imagines Microbiome Experimentation with New Launch – PR Web

Bacteria prevents mosquitoes from spreading Zika, UW-Madison study says – Wisconsin State Journal

Study sheds more light on how bacteria rapidly causes infectious diseases – News Medical

Gut bacteria spotted eating brain chemicals for the first time – Andy Coghlan – New Scientist

Large Grant to Research on Bacteria in the Nose – Statens Serum Institute

Science, publishing, and career

Great and funny read: Some things you need to know about Google Scholar – Mark Dingemans – Ideophone

June 29, 2016

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Two new papers on multiple sclerosis and breast tissue, cross-respiration, the Boston urban transit microbiome, and plastic debris.

Human respiratory microbiome

Review: The respiratory microbiome of HIV-infected individuals – MB Lawawni – Expert Review of Anti-infective Therapy

Human skin microbiome

The microbiota of breast tissue and its association with tumours – Camilla Urbaniak – Applied and Environmental Microbiology

Human gut microbiome

Alterations of the human gut microbiome in multiple sclerosis – Sushrut Jangi – Nature Communications

Review: Gut microbiota and hematopoietic stem cell transplantation: where do we stand? – D Zama – Bone Marrow Transplantation

Review: The neuropharmacology of butyrate: The bread and butter of the microbiota-gut-brain axis? – Roman M. Stilling – Neurochemistry International

Animal and in vitro experiments

A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration – Apollo Stacy – mBio

Press: Cross-respiration between oral bacteria leads to worse infections – EurekAlert

Microbiota-Regulated IL-25 Increases Eosinophil Number to Provide Protection during Clostridium difficile Infection – Erica L. Buonomo – Cell Reports

Animal microbiome

Genome-wide survey of gut fungi (Harpellales) reveals the first horizontally transferred ubiquitin gene from a mosquito host – Yan Wang – Molecular Biology and Evolution

In barn swallows: Stress response, gut microbial diversity and sexual signals correlate with social interactions – Iris I. Levin – Biology Letters

Plant, root, and soil microbiome

Plant Host and Geographic Location Drive Endophyte Community Composition in the Face of Perturbation – Natalie Christian – Microbial Ecology

Perspective: Soil immune responses – Jos M. Raaijmakers – Science

Water and extremophile microbiome

Microbes in mercury-enriched geothermal springs in western North America – Gill G. Geese – Science of The Total Environment

Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton – Cristina M. Herren – mSystems

Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments – Marina N. Mato – Environmental Microbiology

Built environment microbiome

Commentary: Avoiding Pandemic Fears in the Subway and Conquering the Platypus – A. Gonzalez – mSystems

Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment – Tiffany Hsu – mSystems

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

Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre – Jessica A. Bryant – mSystems

Food microbiology

Culture-independent bacterial community profiling of carbon dioxide treated raw milk – Raquel Lo – International Journal of Food Microbiology

Metagenomics and bioinformatics

MetaPalette: a k-mer Painting Approach for Metagenomic Taxonomic Profiling and Quantification of Novel Strain Variation – David Koslicki – mSystems

Bayesian identification of bacterial strains from sequencing data – Aravind Sankar – Microbial Genomics

MetaTreeMap: An Alternative Visualization Method for Displaying Metagenomic Phylogenic Trees – Maxime Hebrard – PLOS ONE

Proteomics and metabolomics

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses – Ernesto S. Nakayasu – mSystems

An Integrated Metabolomic and Genomic Mining Workflow To Uncover the Biosynthetic Potential of Bacteria – Maria Maansson – mSystems

Techniques

16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform – Fiona Fouhy – BMC Microbiology

Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies – Se Jin Song – mSystems

Moleculo Long-Read Sequencing Facilitates Assembly and Genomic Binning from Complex Soil Metagenomes – Richard Allen White III – mSystems

A Universal Next-Generation Sequencing Protocol To Generate Noninfectious Barcoded cDNA Libraries from High-Containment RNA Viruses – Lindsey A. Moser- mSystems

Fungal identification biases in microbiome projects – Leho Tedersoo – Environmental Microbiology Reports

Microbes in the news

Germs in the Subway Are the Harmless Kind – Nicholas Bakalar – New York Times

An Industrial Microbiologist Who Adds Biofuel to the Fire – Nandita Jayaraj – The Wire India

Interview of Faculty of Clinical Microbiology, Prof. Generalov Igor Ivanovich, at VSMU, Belarus – LinkedIn

 

June 28, 2016

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A fundraiser to study the turtle microbiome, multiple sclerosis, generalists inside specialist, and visualizing translational activity.

Events

IndieGoGo campaign: TurtleTracts: Study Microbes to Save Sea Turtles – Aubrey Tauer

Also see this blog post: Sneak Peak at our Sea Turtle Microbiome Initiative – Aubrey Tauer

Pregnancy and birth

Gut bacteria and late-onset neonatal bloodstream infections in preterm infants – Phillip I. Tarr – Seminars in Fetal and Neonatal Medicine

Human respiratory microbiome

Commentary: Mode of delivery to the brave new (microbial) world: a defining moment for the respiratory microbiome? – Georgios D. Kitsios – EBioMedicine

Human gut microbiome

Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls – Jun Chen – Scientific Reports

Press: Link between gut bacteria, MS discovered. MS patients show lower levels of good bacteria – Science Daily

Review: Microbiota as Therapeutic Targets – Xavier R.J. – Digestive Diseases

Animal microbiome
The Generalist Inside the Specialist: Gut Bacterial Communities of Two Insect Species Feeding on Toxic Plants Are Dominated by Enterococcus sp. – Cristina Vilanova – Frontiers in Microbiology

Review: The gut microbiome as a virtual endocrine organ with implications for farm and domestic animal endocrinology – T.F. O’Callaghan – Domestic Animal Endocrinology

Plant, root, and soil microbiome
Systemic enrichment of antifungal traits in the rhizosphere microbiome after pathogen attack – Jan-Hendrik Dudenhöffer – Journal of Ecology

A multi-biological assay approach to assess microbial diversity in arsenic (As) contaminated soils – S.R. Stazi – Geomicrobiology Journal

Effects of two fungicide formulations on microbial and macroinvertebrate leaf decomposition under laboratory conditions – Adria A. Elskus – Environmental Toxicology and Chemistry

Book: Plant, Soil and Microbes – Editors: Khalid Rehman Hakeem, Mohd Sayeed Akhtar – Springer

Water and extremophile microbiome

Metagenomics-Guided Mining of Commercially Useful Biocatalysts from Marine Microorganisms – A.R. Uria – Advances in Food and Nutrition Research

Lessons learned from thirty years of geomicrobiological studies of Río Tinto – Ricardo Amils – Research in Microbiology

Metabolic diversity and adaptive mechanisms of iron- and/or sulfur-oxidizing autotrophic acidophiles in extremely acidic environments – Xian Zhang – Environmental Microbiology Reports

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill – Nina Dombrowski – Nature Microbiology

News and views: Marine microbiology: Community clean up – Rachel Mackelprang – Nature Microbiology

Assessing viral taxonomic composition in benthic marine ecosystems: reliability and efficiency of different bioinformatic tools for viral metagenomic analyses – M. Tangherlini – Scientific Reports

Marine phage genomics: the tip of the iceberg – Blanca Perez Sepulveda – Microbiology Letters

Metabolic networks and proteomics

MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota – Xu Zhang – Microbiome

The use of propidium monoazide in conjunction with qPCR and Illumina sequencing to identify and quantify live yeasts and bacteria – Mansak Tantikachornkiata – International Journal of Food Microbiology

Protocol: Constructing and Analyzing Metabolic Flux Models of Microbial Communities – José P. Faria – Springer Protocols

Viruses and phages

Opinion: The Janus-Face of Bacteriophages across Human Body Habitats – Adam Wahida – PLOS Pathogens

Review: Research on the human virome: where are we and what is next – Shimian Zou – Microbiome

Microbial ecology and techniques

Visualizing in situ translational activity for identifying and sorting slow-growing archaeal−bacterial consortia – Roland Hatzenpichler – PNAS

Press: See and sort: Developing novel techniques to visualize uncultured microbial cell activity – Science Daily

High functional diversity stimulates diversification in experimental microbial communities – Alexandre Jousset – Science Advances

Measuring the biodiversity of microbial communities by flow cytometry – Ruben Props – Methods in Ecology and Evolution

Highlight: A timely reminder of technical limitations – James I. Prosser – Microbial Biotechnology

Species-sorting and mass-transfer paradigms control managed natural metacommunities – Susanne Günther – Environmental Microbiology

Microbes in the news

Slimy clumps of bacteria kill thousands. Scientists are fighting back – Usha Lee McFarling – STAT News

Why everyone’s suddenly talking about gut bacteria – Laura Entis – Fortune

Scientists find link between makeup of individual’s microbiome and head and neck cancer – News Medical

June 26, 2016

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Pregnancy and birth

A key genetic factor for fucosyllactose utilization affects infant gut microbiota development – Takahiro Matsuki – Nature Communications

Necrotizing enterocolitis and preterm infant gut bacteria – Barbara B. Warner – Seminars in Fetal & Neonatal

Human oral microbiome

Identification of Veillonella Species in the Tongue Biofilm by Using a Novel One-Step Polymerase Chain Reaction Method – Izumi Mashima – PLOS ONE

Human respiratory microbiome

Bacterial Microbiota Analysis Present in the Nose and Pharynx of a Mexican Young Population – Ana Karina Rodríguez-Vicente – Int J Curr Microbiol App Sci

Human gut microbiome

Significant Differences Found in Short Nucleotide Sequences of Human Intestinal Metagenomes of Northern-European and Chinese Origin – Balázs Szalkai – Biochimica et Biophysica Acta (BBA) – General Subjects

Analysis of the effects of microbiome-related confounding factors on the reproducibility of the volatolomic test – Marcis Leja – Journal of Breath Research

Campylobacter concisus utilizes blood but not short chain fatty acids despite showing associations with Firmicutes taxa – Nadeem O. Kaakoush – Microbiology

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

Review: Microbiome, Metabolome and Inflammatory Bowel Disease – Ishfaq Ahmed – Microorganisms

Comment: Ethics of exploring the microbiome of native peoples – Maria G. Dominguez-Bello – Nature Microbiology

Microbes found in blood

I’m skeptical about this review: A Bacterial Component to Alzheimer’s-Type Dementia Seen via a Systems Biology Approach that Links Iron Dysregulation and Inflammagen Shedding to Disease – Etheresia Pretorius – Journal of Alzheimer’s Disease

Animal experiments

A sentinel goblet cell guards the colonic crypt by triggering Nlrp6-dependent Muc2 secretion – George M. H. Birchenough – Science

Gut microbiota drive the development of neuro-inflammatory response in cirrhosis – Dae Joong Kang – Hepatology

Bacteriophage infections of microbiota can lead to leaky gut in an experimental rodent model – George Tetz – Gut Pathogens

The Effects of LW-AFC on Intestinal Microbiome in Senescence-Accelerated Mouse Prone 8 Strain, a Mouse Model of Alzheimer’s Disease – Jianhui Wang – Journal of Alzheimer’s Disease

Microbiome associations in pigs with the best and worst clinical outcomes following co-infection with porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) – Megan C. Niederwerder – Veterinary Microbiology

Press: College of Veterinary Medicine researchers examine microbiome associations related to disease expression in swine – Kansas State University

Supplementing Blends of Sugars, Amino Acids, and Secondary Metabolites to the Diet of Termites (Reticulitermes flavipes) Drive Distinct Gut Bacterial Communities – Xing-Feng Huang – Microbial Ecology

Letter: Does Intestinal Microbiota Protect Mice Against Acute/Binge Drinking-Induced Liver Injury? – Tao Zeng – Alcoholism: Clinical and Experimental Research

Animal microbiome

DGGE: Influence of Starvation on the Structure of Gut-Associated Bacterial Communities in the Chinese White Pine Beetle (Dendroctonus armandi) – Xia Hu – Forests

Plant, root, and soil microbiome

Effects of temperature variability on community structure in a natural microbial food web – Axel Zander – Global Change Biology

Effectiveness of ecological rescue for altered soil microbial communities and functions – Kadiya Calderón – ISME Journal

Soil drying procedure affects the DNA quantification of Lactarius vinosus but does not change the fungal community composition – Carles Castaño – Mycorrhiza

Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters – Weichen Bao – Scientific Reports

Water and extremophile microbiome

Revealing the relationship between microbial community structure in natural biofilms and the pollution level in urban rivers: a case study in the Qinhuai River Basin, Yangtze River Delta – Wei Cai – Water Science and Technology

Status of metal pollution in rivers flowing through urban settlements at Pune and its effect on resident microflora – Neelu Nawani – Biologia

Profiling of Sediment Microbial Community in Dongting Lake before and after Impoundment of the Three Gorges Dam – Wei Huang – Int. J. Environ. Res. Public Health

Bioreactor and wastewater microbiology

Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water – Junying Tang – Ecotoxicology and Environmental Safety

Food microbiology

Effect of Simulated Sanitizer Carryover on Recovery of Salmonella from Broiler Carcass Rinsates – Gary R. Gamble – Journal of Food Protection

Press: USDA Salmonella Bacteria on Chicken Testing Severely Flawed, New Study Finds – Emily Monaco – Organic Authority

Potential applications of metagenomics to assess the biological effects of food structure and function – Tasha Santiago-Rodriguez – Food & Function

Bioinformatics and metagenomics

A comparison of tools for the simulation of genomic next-generation sequencing data – Merly Escalona – Nature Reviews Genetics

Hessian Regularization Based Symmetric Nonnegative Matrix Factorization for Clustering Gene Expression and Microbiome Data – Yuanyuan Ma – Methods

Techniques

Grown, Printed, and Biologically Augmented: An Additively Manufactured Microfluidic Wearable, Functionally Templated for Synthetic Microbes – Christoph Bader – 3D Printing and Additive Manufacturing

Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning – Lucia Kraková – Extremophiles

DGGE: Representative sampling of natural biofilms: influence of substratum type on the bacterial and fungal communities structure – Jennifer Hellal – Springer Plus

More microbiology

Applying landscape genetics to the microbial world – Rachael Y. Dudaniec – Molecular Ecology

A metapopulation model for the spread of MRSA in correctional facilities – Marc Beauparlant – Infectious Disease Modelling

Biological Dual-Use Research and Synthetic Biology of Yeast – Angela Cirigliano – Science and Engineering Ethics

Microbes in the news

Fabulous Pacific coast and the latest digestive diseases research: BMC Medicine joins DDW2016 – Alessandro Recchioni – BioMedCentral blog

The Unseen – Millions of microbes are yet to be discovered. Will one hold the ultimate cure? – Raffi Khatchadourian – The New Yorker

Indicator of chronic fatigue syndrome found in gut bacteria – Krishna Ramanujan – Cornell Chronicle

Fermentation Fervor: Here’s How Chefs Boost Flavor And Health – Allison Aubrey – NPR Morning Edition

Beneficial bacteria may protect breasts from cancer – ASM – EurekAlert

Economics in Mind, Evolution Has Allowed Some Bacteria to Evolve Sublime Genomes – Aswin Sai Narain Seshasayee – The Wire

Old Technology Successfully Reduce Salmonella in Meat Products by 90 Percent –  John Raphael – Nature World News

Bright Minds Battling Dark Diseases: San Diego is home to world-class biomedical scientists focused on cutting-edge projects touted by president – Gary Robbins – The San Diego Union Tribune

Liquid eyeliner recalled, contains bacteria – CTV News Winnipeg

June 23, 2016

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Red snow microbiomes and melting glaciers, effect of earthworms on microbes, microbiome in COPD.

Pregnancy and birth

Early Gut Microbiota Perturbations Following Intrapartum Antibiotic Prophylaxis to Prevent Group B Streptococcal Disease – Giuseppe Mazzola – PLOS ONE

Human respiratory microbiome

Editorial: Early life nasal microbiota in infants with cystic fibrosis – Fiona J Whelan – The Lancet Respiratory Medicine

Review: Understanding the role of the microbiome in COPD: Principles, Challenges and Future Directions – Yvonne J. Huang – Translational Research

Human gut microbiome

Anaerococcus rubiinfantis sp. nov., isolated from the gut microbiota of a Senegalese infant with severe acute malnutrition – Maryam Tidjani Alou – Anaerobe

Review: Understanding the mechanisms of faecal microbiota transplantation – Alexander Khoruts – Nature Reviews Gastroenterology & Hepatology

Review: Microbe-host interactions: Influence of the gut microbiota on the enteric nervous system – Niall P. Hyland – Developmental Biology

Systematic review: Probiotic supplementation can positively affect anxiety and depressive symptoms: a systematic review of randomized controlled trials – Meysam Pirbaglou – Nutrition Research

Animal experiments

Maternal gut and fetal brain connection: Increased anxiety and reduced social interactions in Wistar rat offspring following peri-conceptional antibiotic exposure – Stéphanie Degroote – Progress in Neuro-Psychopharmacology and Biological Psychiatry

A human gut ecosystem protects against C. difficile disease by targeting TcdA – Sarah Lynn Martz – Journal of Gastroenterology

Animal microbiome

Species-specific effects of earthworms on microbial communities and the fate of litter-derived carbon – Chih-Han Chang – Soil Biology and Biochemistry

Diversity of natural product biosynthetic genes in the microbiome of the deep sea sponges Inflatella pellicula, Poecillastra compressa and Stelletta normani – Alan D. Dobson – Frontiers in Microbiology

Plant, root, and soil microbiome

Tree species select diverse soil fungal communities expressing different sets of lignocellulolytic enzyme-encoding genes – Florian Barbi – Soil Biology and Biochemistry

Repeated annual glyphosate applications may impair beneficial soil microorganisms in temperate grassland – M. Druille – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

 The biogeography of red snow microbiomes and their role in melting arctic glaciers – Stefanie Lutz – Nature Communications

Press: The Arctic’s pretty but alarming strawberry-pink snow – Ben Guarino – Washington Post
This Pink Snow Does Not Bode Well For Our Future – Maddie Stone – Gizmodo

Effects of heap-bioleaching plant on microbial community of the nearby river – Mingjiang Zhang – International Biodeterioration & Biodegradation

Molecular Characterization of Aquatic Bacterial Communities in Dinaric Range Caves – Pleše, Bruna – Water Environment Research

Air microbiome

High-throughput sequencing reveals unprecedented diversities of Aspergillus species in outdoor air – Seungeun Lee – Letters in Applied Microbiology

Food microbiology

Changes in the microbiota of lamb packaged in a vacuum and in modified atmospheres during chilled storage analysed by high-throughput sequencing – Taojun Wang – Meat Science

Microbial Diversity of Type I Sourdoughs Prepared and Back-Slopped with Wholemeal and Refined Soft (Triticum aestivum) Wheat Flours – Manuela Taccari – Journal of Food Science

Added ingredients affect the microbiota and biochemical characteristics of durum wheat type-I sourdough – Fabio Minervini – Food Microbiology

Fungal diversity and ecosystem function data from wine fermentation vats and microcosms – Primrose J. Boynton – Data in Brief

The phenotypic characterization of yeast strains to stresses inherent to wine fermentation in warm climates – M. García – Journal of Applied Microbiology

Built environment microbiology

Contamination of healthcare workers’ mobile phones by epidemic viruses – S. Pillet – Clinical Microbiology and Infection

Press: Mobile devices of healthcare workers often contaminated by viral RNA – News Medical

No access for me, but intriguing title: Show research into the human microbiome can be used to solve crimes – Kyle Nothern – Southern California Interdisciplinary Law Journal

Microbes in the news
Video: Citizen Science and Mapping the Microbiome – Eric J. Topol interviews Jessica Richman – Medscape

Mapping the subway’s microbiome. Barcelona takes part in the international research project Metasub, which aims to map the microbiome of public transit systems in 54 cities worldwide – EurekAlert

Biology professor helps author free textbook, saving students hundreds: OpenStax Microbiology – Lainie Mazzullo – Wichita State University

Science, publishing, and career

At 31, she runs one of the hottest biotech companies in the country, with Rachel Haurwitz, CEO of Caribou Biosciences – Andrew Joseph – STAT news

Stem cell scientist Paolo Macchiarini suspected of involuntary manslaughter – STAT news

June 17, 2016

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Gastric bypass induces persistent gut microbiome changes, omnivorous lizards going vegetarian, new Borrelia species in Australian ticks, a free-living Bradyrhizobium, plant responses to phyllosphere commensals, and chemotrophic microbial populations in Yellowstone hot springs.

Events

HT: Jonathan Eisen: June 20-21 Meeting #2 for NAS Microbiomes of the Built Environment Study. Click here to register for the webcast (free!).

Human respiratory microbiome

Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children – Marcos Pérez-Losada – Microbiome

Human gut microbiome

Antibiotic-induced gut microbiota disruption during human endotoxemia: a randomised controlled study – Jacqueline M Lankelma – Gut
Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota – Albert Palleja – Genome Medicine

Review: Metabolomics of autism spectrum disorders: early insights regarding mammalian-microbial cometabolites – Michele Mussap – Expert Review of Molecular Diagnostics

Review: How the microbiota shapes rheumatic diseases – Tom Van de Wiele – Nature Reviews Rheumatology

Animal and other experiments

Physiological and microbial adjustments to diet quality permit facultative herbivory in an omnivorous lizard – Kevin D. Kohl – Journal of Experimental Biology

Press: How does a lizard go vegetarian? By growing its gut – Patrick Monahan – Science Magazine

Nasal commensal Staphylococcus epidermidis counteracts influenza virus – Hui-Wen Chen – Scientific Reports

Animal microbiome

Diversity, structure and convergent evolution of the global sponge microbiome – Torsten Thomas – Nature Communications

Does canine inflammatory bowel disease influence gut microbial profile and host metabolism? – Jia Xu – BMC Veterinary Research

Novel Borrelia species detected in echidna ticks, Bothriocroton concolor, in Australia – Siew-May Loh – Parasites & Vectors

Press: New bacteria discovered in Australian ticks – MedicalXpress

Plant, root, and soil microbiome

Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes – a genome comparison – Frances Patricia Jones – Scientific Reports

Press: Study unlocks surprising behaviour of soil bacteria – Mark Kinver – BBC

The Arabidopsis leaf transcriptome reveals distinct but also overlapping responses to colonization by phyllosphere commensals and pathogen infection with impact on plant health – Christine Vogel – New Phytologist

DNA from dust: comparative genomics of vaccine-break virus in the field – Utsav Pandey – bioRxiv

Water and extremophile microbiome

Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs – Daniel R. Colman – FEMS Microbiology Ecology

Large shifts among eukaryotes, bacteria, and archaea define the vertical organization of a lake sediment – Christian Wurzbacher – bioRxiv

Microbes in the news

Featuring an All Male Panel: That Gut Feeling: Part One. Dan Saladino discovers the world of the gut microbiota, the vast array of microbes within us all – BBC Radio

Bik’s Picks

Klinefelter’s syndrome (47,XXY) is in excess among men with Sjögren’s syndrome –
Valerie M. Harris – Clinical Immunology

Press: Does X mark the spot? A new clue why autoimmune diseases target women – Oklahoma Medical Research Foundation

June 16, 2016

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ASM Microbe 2016 meeting Tweet-up, two exciting papers on infant gut colonization, Lactobacillus reuteri restores autism-like behavior in a mouse model, rumen microbiomes in high-altitude mammals, an undergraduate lab in food spoilage, the archaeal origins of eukaryotes, and the discovery of CRISPRs.

Events

ASM Microbe 2016 Tweet-up is Friday, June 17, 11:45-12:30 in the Peer-to-Peer Exchange Zone (in the Exhibition Hall)

Pregnancy and birth

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability – Moran Yassour – Science Translational Medicine

Antibiotics, birth mode, and diet shape microbiome maturation during early life – Nicholas A. Bokulic – Science Translational Medicine

Press: Antibiotics given to babies change their gut microbes for years – Anna Vlasits – STAT
Don’t Stress About Your Baby’s Microbiome Just Yet. Antibiotics and C-sections might change a baby’s microbes, but it’s not clear that those changes are bad, lasting, or that they matter at all. – Ed Yong- the Atlantic

Research Highlight: Growing up together — gut microbiota assembly and IgA – Hugh Thomas – Nature Reviews Gastroenterology & Hepatology

Opinion: Why Don’t All Infants Have Bifidobacteria in Their Stool? – Gerald W. Tannock – Frontiers in Microbiology

Human oral microbiome
A preliminary study of the oral microbiota in Chinese patients with Sjögren’s Syndrome – Miaoran Li – Archives of Oral Biology

Detection of Novel Integrons in the Metagenome of Human Saliva – Supathep Tansirichaiya – PLOS ONE

Human respiratory microbiome

Severe Achromobacter xylosoxidans infection and loss of sputum bacterial diversity in an adult patient with cystic fibrosis – Nick P. Talbot – Paediatric Respiratory Reviews

Human gut microbiome

Occurrence of human sapoviruses in wastewater and stool samples in Rio de Janeiro, Brazil – Julia Monassa Fioretti – Journal of Applied Microbiology

Review: Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism – Annika Wahlström – Cell Metabolism

Review: Repertoire of human gut microbes – Perrine Hugon – Microbial Pathogenesis

Review: The intestinal microbiome and surgical disease – Monika A. Krezalek – Current Problems in Surgery

Animal experiments

Microbial Reconstitution Reverses Maternal Diet-Induced Social and Synaptic Deficits in Offspring – Shelly A. Buffington – Cell

Press: A single species of gut bacteria can reverse autism-related social behavior in mice – MedicalXpress
Single Bacterial Species Improves Autism-Like Behavior in Mice – Ruth Williams – The Scientist

Absence of gut microbiota influences lipopolysaccharide-induced behavioral changes in mice – Alline C. Campos – Behavioural Brain Research

Altered Microbiota Contributes to Reduced Diet-Induced Obesity upon Cold Exposure –
Marika Ziętak – Cell Metabolism

Revealing the combined effects of lactulose and probiotic enterococci on the swine faecal microbiota using 454 pyrosequencing – Jong Pyo Chae – Microbial Biotechnology

Lactobacillus rhamnosus GG modulates innate signaling pathway and cytokine responses to rotavirus vaccine in intestinal mononuclear cells of gnotobiotic pigs transplanted with human gut microbiota – Haifeng Wang – BMC Microbiology

Effect of postnatal low-dose exposure to environmental chemicals on the gut microbiome in a rodent model – Jianzhong Hu – Microbiome

Animal microbiome

Multiyear Survey of Coccidia, Cryptosporidia, Microsporidia, Histomona, and Hematozoa in Wild Quail in the Rolling Plains Ecoregion of Texas and Oklahoma, USA – Lixin Xiang – The Journal of Eukaryotic Microbiology

Convergent Evolution of Rumen Microbiomes in High-Altitude Mammals – Zhigang Zhang – Current Biology

Plant, root, and soil microbiome

Biogeographical patterns in fungal communities from soils cultivated with sugarcane – Thiago Gumiere – Journal of Biogeography

Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities – S. Uroz – Scientific Reports

Inoculant of Arbuscular Mycorrhizal Fungi (Rhizophagus clarus) Increase Yield of Soybean and Cotton under Field Conditions – Martha V. T. Cely – Frontiers in Microbiology

Patterns and drivers of soil microbial communities in Tibetan alpine and global terrestrial ecosystems – Yong-Liang Chen – Journal of Biogeography

Water and extremophile microbiome

Microbial Inventory of Deeply Buried Oceanic Crust from a Young Ridge Flank – Steffen L. Jørgensen – Frontiers in Microbiology

Resilience of Freshwater Communities of Small Microbial Eukaryotes Undergoing Severe Drought Events – Marianne Simon – Frontiers in Microbiology

Food microbiology

Undergraduate Laboratory Exercises Specific to Food Spoilage Microbiology – Abigail B. Snyder – Journal of Food Science Education

Waste and pollution microbiology

Comparison of microbial taxonomic and functional shift pattern along contamination gradient – Youhua Ren – BMC Microbiology

More microbiology

On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype: A Hunt for the Archaeal Ancestor of Eukaryotes – Gautam Dey – Trends in Cell Biology

Press: Life as we know it most likely arose via ‘long, slow dance’ – EurekAlert

Mentions our Mycobacterium paper from 1991! The discovery of CRISPR in archaea and bacteria – Francisco J. M. Mojica – The FEBS Journal

Microbes in the news

Antibiotics increase availability of nutrients in the gut, enabling growth of pathogens, with Franziska Faber – UC Davis – Science Daily

Whole Foods Must Clean Up Its Act, FDA Says. Agency warns of ‘serious violations’ at food-preparation plant – Jesse Newman and Heather Haddon – Wall Street Journal

The Parasite Underground – A shadow network of patients are trying to treat their own debilitating diseases — by infecting themselves with gastrointestinal worms – Moises Velasquez-Manoff – The New York Times Magazine

uBiome Doubles Research Grant to Award Two Microbiome Researchers up to $100,000 Each – PR Web

About MetaFast: Personalized medicine will employ computer algorithms – Science Daily

University Seeks to Capitalize on Push to Harness Helpful Microbes – In more recent years, microbes have proved their worth through things like polymerase chain reaction – Terry Devitt – University of Wisconsin-Madison

TGen test shows promise for diagnosing Lyme – Emery Cowan – AZ Daily Sun

Important opinion piece: We are not viruses: Don’t limit gay men from donating blood – Benjamin Mazer – STAT news

Satire: New Mountain Dew Vows To Kill 99.9% Of Stomach Bacteria – The Onion

Science, publishing, and career

A peek at peer review helps young scientists – Jeffrey Mervis – Science

The age of the Twitter conference – Stephanie Avery-Gomm – Science

June 15, 2016

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Microbiome evolution in vertebrates, post-antibiotic microbial competition for sugars, microbial networks in respiratory infections, bacteria in snow from Australian and Swiss Alps, Yucatan Black and Red soil microbes.

Human oral microbiome

Longitudinal assessment of sputum microbiome by sequencing of the 16S rRNA gene in non-CF bronchiectasis patients – Michael J Cox – bioRxiv

Human skin microbiome

Comprehensive pyrosequencing analysis of the bacterial microbiota of the skin of patients with seborrheic dermatitis – Akiomi Tanaka – Microbiology and Immunology

Review: Can molecular DNA-based techniques unravel the truth about diabetic foot infections? – M. Malone – Diabetes/Metabolism Research and Reviews

Human respiratory microbiome

Mycoplasma pneumoniae and Streptococcus pneumoniae caused different microbial structure and correlation network in lung microbiota – Heping Wang – Journal of Thoracic Disease

Human gut microbiome

Ecophysiological consequences of alcoholism on human gut microbiota: implications for ethanol-related pathogenesis of colon cancer – Atsuki Tsuruya – Scientific Reports

Research highlight: Intimate gut interactions: helminths and the microbiota – Nicola L Harris – Cell Research

Review: Human Gut-on-a-Chip technology: Will this revolutionize our understanding of IBD and future treatments? – Jaewon Lee – Expert Review of Gastroenterology & Hepatology

Review: Dientamoeba fragilis, the Neglected Trichomonad of the Human Bowel – Damien Stark – Clinical Microbiology Reviews

Review: Akkermansia muciniphila: a novel functional microbe with probiotic properties – C. Gómez-Gallego – Beneficial Microbes

Review: Alterations of gut microbiota in patients with irritable bowel syndrome: A systematic review and meta-analysis – Xiaojun Zhuang – Journal of Gastroenterology and Hepatology

Animal and tissue culture experiments

Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion – Franziska Faber – Nature

News and Views: Microbiology: The dark side of antibiotics – Thibault G. Sana & Denise M. Monack – Nature

Genetic and transcriptional analysis of human host response to healthy gut microbiome – Allison L Richards – bioRxiv

The Microbiota Determines Susceptibility to Experimental Autoimmune Uveoretinitis – Jarmila Heissigerova – Journal of Immunology Research

Animal microbiome

Invited Review: Microbiome Evolution Along Divergent Branches of the Vertebrate Tree of Life: What’s Known and Unknown – Timothy J. Colston – Molecular Ecology

Microbial community structure of two freshwater sponges using Illumina MiSeq sequencing revealed high microbial diversity – Swapnil Gaikwad – AMB Express

Plant, root, and soil microbiome

Endophytic bacterial and fungal microbiota in sprouts, roots and stems of rice (Oryza sativa L.) – Wenfeng Wang – Microbiological Research

Yucatán in black and red: Linking edaphic analysis and pyrosequencing-based assessment of bacterial and fungal community structures in the two main kinds of soil of Yucatán State – Héctor Estrada-Medina – Microbiological Research

Water and extremophile microbiome

Global and local-scale variation in bacterial community structure of snow from the Swiss and Australian Alps – Tina Wunderlin – FEMS Microbiology Ecology

Waste, pollution, drinking water microbiology

Assessing the effects of heavy metals in ACC deaminase and IAA production on plant growth-promoting bacteria – Mendoza-Hernández José Carlos – Microbiological Research

Effect of Co-Composting Cattle Manure with Construction and Demolition Waste on the Archaeal, Bacterial, and Fungal Microbiota, and on Antimicrobial Resistance Determinants – Devin B. Holman – PLOS ONE

Anthropogenic impact on mangrove sediments triggers differential responses in the heavy metals and antibiotic resistomes of microbial communities – Lucélia Cabral – Environmental Pollution

Investigation of Archaeal and Bacterial community structure of five different small drinking water networks with special regard to the nitrifying microorganisms – Zsuzsanna Nagymáté – Microbiological Research

A survey of biofilms on wastewater aeration diffusers suggests bacterial community composition and function vary by substrate type and time – Peter A. Noble – Applied Microbiology and Biotechnology

DGGE: Synergistic effect of crude oil plus dispersant on bacterial community in a louisiana salt marsh sediment – Mohammed Al-Jawasim – FEMS Microbiology Letters

Food microbiology

Complexity and Dynamics of the Winemaking Bacterial Communities in Berries, Musts, and Wines from Apulian Grape Cultivars through Time and Space – Marinella Marzano – PLOS ONE

More microbiology

Viruses Infecting a Freshwater Filamentous Cyanobacterium (Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B – Caroline Chénard – mBio

Press: Virus Hacks Host Genome, Steals CRISPR to Protect Itself – GenEngNews
Virus uses ‘stolen’ CRISPR to hack its host’s immune system – Science Daily

Microbes in the news

Asgard archaea diversity in estuaries – Roy Rodriguez – REU in Subtropical Marine Ecosystems, University of Texas at Austin

Microbes in pressed grapes may predict flavor metabolites in the finished wine – American Society for Microbiology – EurekAlert

Nanoflowers can detect bacteria before they make you sick: The particles can spot even tiny amounts of E. coli – Mariella Moon – Engadget

BacteriaHysteria: Self-cleaning sheets do exist! Silvon launches bacteria-resistant bedding – Julie Pennell – Today

Science, publishing, and career

Predatory journals: Ban predators from the scientific record – Jeffrey Beall – Nature

Data sharing: A code of conduct for data on epidemics – Ilaria Capua – Nature

June 7, 2016

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Microbiomes of the lung, red coral, effect of invertebrates on water microbes, and bacteriophages are reservoirs of antibiotic resistance genes.

General microbiome

The vast unknown microbial biosphere – Carlos Pedrós-Alió – PNAS

Human respiratory microbiome

Review: The Lung Microbiome, Immunity, and the Pathogenesis of Chronic Lung Disease – David N. O’Dwyer – The Journal of Immunology

Review/Hypothesis: A Role for the Intestinal Microbiota and Virome in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)? – Navena Navaneetharaja – MDPI Journal of Clinical Medicine

Human gut microbiome

Review: The metabolic role of the gut microbiota in health and rheumatic disease: mechanisms and interventions – Shahla Abdollahi-Roodsaz – Nature Reviews Rheumatology

Animal experiments

Accelerated dysbiosis of gut microbiota during aggravation of DSS-induced colitis by a butyrate-producing bacterium – Qianpeng Zhang – Scientific Reports

Bacterial Adrenergic Sensors Regulate Virulence of Enteric Pathogens in the Gut – Cristiano G. Moreira – mBio

Animal microbiome

Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum on a broad geographic scale – Jeroen A. J. M. van de Water – Scientific Reports

Plant, root, and soil microbiome

Mangrove succession enriches the sediment microbial community in South China – Quan Chen – Scientific Reports

Correlations between the composition of modular fungal communities and litter decomposition-associated ecosystem functions – Witoon Purahong – Fungal Ecology

History Leaves Its Mark on Soil Bacterial Diversity – Jennifer B. H. Martiny – mBio

Water and extremophile microbiome

Alteration of physico-chemical and microbial properties in freshwater substrates by burrowing invertebrates – Carolin Boeker – Limnologica – Ecology and Management of Inland Waters

Effects of the invasive clam Corbicula fluminea (Müller, 1774) on an estuarine microbial community – Adriana Novais – Science of The Total Environment

Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria – Gregory K. Farrant – PNAS

Bacterial community composition and structure in an Urban River impacted by different pollutant sources – A. Mark Ibekwe – Science of The Total Environment

Population Dynamics and Community Composition of Ammonia Oxidizers in Salt Marshes after the Deepwater Horizon Oil Spill – Anne Bernhard – Frontiers in Microbiology

Review: Cannibalistic viruses in the aquatic environment: role of virophages in manipulating microbial communities – V. Marie – International Journal of Environmental Science and Technology

Built environment microbiome

Molecular investigation of bacterial communities: Data from two frequently used surfaces in the São Paulo Institute of Tropical Medicine – Tairacan Augusto Pereira da Fonseca – Data in Brief

The prevalence of foodborne pathogenic bacteria on cutting boards and their ecological correlation with background biota – Noor-Azira Abdul-Mutalib – AIMS Microbiology

Metagenomics and viruses

Metagenomic analysis reveals that bacteriophages are reservoirs of antibiotic resistance genes – Jéssica Subirats – International Journal of Antimicrobial Agents

Bioinformatics

SMART: Statistical Metabolomics Analysis—An R Tool – Yu-Jen Liang – Analytical Chemistry

Techniques

Book: Field Guidelines for Genetic Experimental Designs in High-Throughput Sequencing – Editors: Ana M. Aransay, José Luis Lavín Trueba – Springer Books

More microbiology

Coupling spatiotemporal community assembly processes to ecosystem function – Emily Graham – PeerJ Preprint

Evolution of the archaeal and mammalian information processing systems: towards an archaeal model for human disease – Zhe Lyu – Cellular and Molecular Life Sciences

Species richness influences wine ecosystem function through a dominant species – Primrose J. Boynton – Fungal Ecology

Microbes in the news
New antimicrobial material joins fight against antibiotic-resistant bacteria – Michael Irving – GizMag

Note: PNAS paper not yet out: Distinguishing Deadly Staph Bacteria from Harmless Strains – Heather Buschman – UC San Diego

Scientists craft an artificial seawater concoction. New recipe facilitates marine microbe cultivation and characterization – EurekAlert

The man who can map the chemicals all over your body: Pieter Dorrestein uses mass spectrometry to eavesdrop on the molecular conversations between microbes and their world – Paul Tullis – Nature

Stockton Kimball Awardee is Noted Bacterial Pathogenesis Researcher – University of Buffalo

MSU doctoral student Jeffrey Simkins awarded National Science Foundation fellowship to research in Australia – Montana State University – KBZK

Vaccine watches bacteria, strikes only when trouble stirs – University of Buffalo

Bacteria hairs make excellent electrical wires – Science Daily

Science, publishing, and career

My paper got published: The Prevalence of Inappropriate Image Duplication in Biomedical Research Publications – Elisabeth M. Bik, Arturo Casadevall, Ferric C. Fang – mBio