Category Archives: Waste and pollution

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 22, 2016

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Nipple aspirate, CNS infections, fiber and food allergies, horses and honeybee bacteria, and a report from the subway citizen science project.

General human microbiome

Commentary: Lessons Learned from Probing for Impacts of Triclosan and Triclocarban on Human Microbiomes – Rolf U. Halden – mSphere

Human nipple microbiome

Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors – Alfred A. Chan – Scientific Reports

Human vaginal microbiome

Impact of Probiotic SYNBIO® Administered by Vaginal Suppositories in Promoting Vaginal Health of Apparently Healthy Women – Maria Cristina Verdenelli – Current Microbiology

Human gut microbiome

Alterations of Intestinal Microbiome by Antibiotic Therapy in Hospitalized Children – Miriam R. Fernandes – Microbial Drug Resistance

Could gut microbiota serve as prognostic biomarker associated with colorectal cancer patients’ survival? A pilot study on relevant mechanism – Zhiliang Wei – Oncotarget

ASM Microbe 2016 abstract: Increased Akkermansia muciniphila and Bacteroides fragilis Group Abundance After Islamic Fasting – C. Erdogdu – ASM Microbe 2016

Press: Happy Ramadan From Your Microbiome! – Gastroenterology & Endoscopy News

Review: Inflammation and the microbiome: implications for depressive disorders – Shawn Hayley – Current Opinion in Pharmacology

Review: Role of the microbiome, probiotics, and ‘dysbiosis therapy’ in critical illness.– Wischmeyer, Paul E. – Current Opinion in Critical Care

Infection and microbiology

Next-generation sequencing in neuropathologic diagnosis of infections of the nervous system – Steven L. Salzberg – Neurology Neuroimmunology & Neuroinflammation

Press: Diagnosing brain infections using metagenomics – Julian Harris – PHG Foundation

Animal experiments

Dietary Fiber and Bacterial SCFA Enhance Oral Tolerance and Protect against Food Allergy through Diverse Cellular Pathways – Jian Tan – Cell Reports

Press: Diet high in fiber and vitamin A key to preventing allergies to peanuts and other triggers – EurekAlert

Gut microbiota translocation to the pancreatic lymph nodes triggers NOD2 activation and contributes to T1D onset – Frederico R.C. Costa – Journal of Experimental Medicine

Cutting Edge: Commensal Microbiota Has Disparate Effects on Manifestations of Polyglandular Autoimmune Inflammation – Camilla H. F. Hansen – The Journal of Immunology

Fighting Off Wound Pathogens in Horses with Honeybee Lactic Acid Bacteria – Tobias C. Olofsson – Current Microbiology

Plant, root, and soil microbiome

Local diversity of heathland Cercozoa explored by in-depth sequencing – Christoffer Bugge Harder – the ISME Journal

Press: Immense species richness of bacterial-eating microorganisms discovered in soil – Phys.org

Characterization of cadmium-resistant bacteria and their potential for reducing accumulation of cadmium in rice grains – Xiaoyan Lin – Science of The Total Environment
Editorial special issue: Soil, plants and endophytes – Stéphane Compant – Plant and Soil

Water and extremophile microbiome

Diverse Sulfur Metabolisms from Two Subterranean Sulfidic Spring Systems – Karen Rossmassler – FEMS Microbiology Letters

Metabolic potential of microbial mats and microbialites: autotrophic capabilities described by an in silico stoichiometric approach from shared genomic resources – Daniel Cerqueda-García – Journal of Bioinformatics and Computational Biology

Waste and pollution microbiology

Microbial contamination along the main open wastewater and storm water channel of Hanoi, Vietnam, and potential health risks for urban farmers – Samuel Fuhrimann – Science of The Total Environment

Isolation of Bdellovibrio bacteriovorus from a tropical wastewater treatment plant and predation of mixed species biofilms assembled by the native community members – Shugeng Feng – Environmental Microbiology

Microbial forensics

Microbial forensics: next‐generation sequencing as catalyst – Irene Kuiper – EMBO Reports

Bioinformatics and metagenomics

MEGAN Community Edition – Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data – Daniel H. Huson – PLOS Computational Biology

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses – François Enault – The ISME Journal

More microbiology

Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing – Justin Jee – Nature

Press: Sequencing method precise enough to reveal mechanisms by which bacteria resist antibiotics – Phys.org

Darwinolide, a New Diterpene Scaffold That Inhibits Methicillin-Resistant Staphylococcus aureus Biofilm from the Antarctic Sponge Dendrilla membranosa – Jacqueline L. von Salm – Organic Letters

Press: Antibiotics from a Sponge. Could a new compound from Antarctic sea sponges be the key to breaching MRSA’s impregnable barricades? – Michael Lucibella – Antarctic Sun

Microbes in the news

MetaSUB Citizen Science Project:
With video of researchers swabbing away: Biologists Study What Kind Of Bacteria Is On New York City Subways – CBS Local
Qiagen, CosmosID Join International Urban Microbiome Project – Genome Web

New Life Found That Lives Off Electricity. Scientists have figured out how microbes can suck energy from rocks. Such life-forms might be more widespread than anyone anticipated – Emily Singer – Quanta Magazine

High-tech program on microbiome-based research launched in Qingdao – Hu Qing – China Daily

Explained: flesh eating bacteria in the Gulf of Mexico – Dylan Baddour – Houston Chronicle

Science, publishing, and career

Your Science Conference Should Have a Code of Conduct – Brett Favaro – Frontiers in Marine Science

Science in China – A special issue looks at the country’s astonishing scientific trajectory as it seeks to secure its spot among the leaders in innovation – Nature
China by the numbers. Research capacity has grown rapidly, and now quality is on the rise – Richard Van Noorden – Nature

Global Research Council: Commit to equity for women researchers – France A. Córdova – Nature

June 20, 2016

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The temperate tree phyllosphere, Qaanaaq Glacier, effect of human activities on Hong Kong coast microbes, and genome assembly from read clouds.

Events

Microbiome R&D and Business Collaboration Forum: USA, October 3-4, San Diego

Pregnancy and birth

Putative periodontopathic bacteria and herpesviruses in pregnant women: a case-control study – Haixia Lu – Scientific Reports

Human gut microbiome

Letter to Editor: Reduction of antibiotic resistance genes in intestinal microbiota of recurrent Clostridium difficile patients after fecal microbiota transplantation – Hanne Jouhten – Clinical Infectious Diseases Advance Access

Review: The Gut Microbiota and Inflammatory Bowel Diseases – Jun Miyoshi – Translational Research

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

Animal models

Interactions between the colonic transcriptome, metabolome and microbiome in mouse models of obesity-induced intestinal cancer – Anna C. Pfalzer – Physiological Genomics

Plant, root, and soil microbiome

Host species identity, site and time drive temperate tree phyllosphere bacterial community structure – Isabelle Laforest-Lapointe – Microbiome

Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations – Quan Li – Scientific Reports

A comparative analysis of microbiomes in natural and anthropogenically disturbed soils of northwestern Kazakhstan – E. V. Pershina – Eurasian Soil Science

A novel isolate and widespread abundance of the candidate alphaproteobacterial order (Ellin 329), in southern Appalachian peatlands – Austin B. Harbison – FEMS Microbiology Letters

Water and extremophile microbiome

Microbial community variation in cryoconite granules on Qaanaaq Glacier, NW Greenland – Jun Uetake – FEMS Microbiology Ecology

Mechanisms driving Antarctic microbial community responses to ocean acidification: a network modelling approach – Roshni C. Subramaniam – Polar Biology

Video article: Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR – Enrico Tatti – Journal of Visualized Experiments

Waste and pollution microbiology

Microorganisms in heavy metal bioremediation: strategies for applying microbial-community engineering to remediate soils – Jennifer L. Wood – AIMS Bioengineering

Impacts of Human Activities on Distribution of Sulfate Reducing Prokaryotes and Antibiotic Resistance Genes in Marine Coastal Sediments of Hong Kong – Feng Guo – FEMS Microbiology Ecology

Shotgun metagenomic profiles have a high capacity to discriminate activated sludge according to wastewater type – Federico M. Ibarbalz – Applied and Environmental Microbiology

Characteristics of Sediment Bacterial Community in Response to Environmental Impacts in a Sewage Polluted River – Jialin Li – Journal of Coastal Research

Plants rather than mineral fertilization shape microbial community structure and functional potential in legacy contaminated soil – Jakub Ridl – Frontiers in Microbiology

Food microbiology

Viable bacterial population and persistence of foodborne pathogens on the pear carpoplane – Francois J. Duvenage – Journal of the Science of Food and Agriculture

Book: Acetic Acid Bacteria: Ecology and Physiology – Springer

Metagenomics and bioinformatics

Genome assembly from synthetic long read clouds – Volodymyr Kuleshov – Bioinformatics

Unsupervised Binning of Metagenomic Assembled Contigs Using Improved Fuzzy C-Means Method – Yun Liu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

Bioreactor microbiology

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion – Inka Vanwonterghem – Environmental Microbiology

Microbes in the news

From ASM Microbe 2016: Bacteria Can Persist on Gloves, Transfer to Surfaces – Neil Osterweil – Medscape

Ischemic stroke therapy – does the gut microbiota hold the key? – Sara Adães – PLOS Neuro Community

French microbiologist hopes CRISPR/Cas9 can be used medically, with Emmanuelle Charpentier – Focus Taiwan

Chipotle Bosses Accused Of Insider Trading During Bacteria Scandals – Scott Heins – Gothamist

Bik’s Not-Microbiology Picks

Why Did Scientists Release Dead Sea Turtles into Chesapeake Bay? – Erica Tennenhouse – The Science Explorer

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 14, 2016

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Breastfeeding protects against antibiotics’ effect in infants, pediatric gut microbiome after surgery, microbial contribution to regional wine characteristics, microbial hotspots on glacial surfaces, foodwebs in your gut, and much more!

Pregnancy and birth

Association of Early-Life Antibiotic Use and Protective Effects of Breastfeeding – 
Role of the Intestinal Microbiota – Katri Korpela – JAMA Pediatrics

Press: Antibiotics May Blunt Breast-Feeding’s Benefits – Infants given the drugs were prone to infections and obesity in childhood, researchers say – WebMD

Human gut microbiome

The pediatric intestinal mucosal microbiome remains altered after clinical resolution of inflammatory and ischemic disease – Minna M. Wieck – Surgery

Press: Culture Crash: How Common Pediatric Diseases Affect the Healthy Intestinal Microbiome – Children’s Hospital Los Angeles

Systematic Review: Fecal Microbiota Transplantation for Ulcerative Colitis: A Systematic Review and Meta-Analysis – Yanqiang Shi – PLOS ONE

Animal and bioreactor experiments

Vancomycin Treatment Alters Humoral Immunity and Intestinal Microbiota in an Aged Mouse Model of Clostridium difficile Infection – Edward van Opstal – Journal of Infectious Diseases

The structural alteration of gut microbiota in low-birth-weight mice undergoing accelerated postnatal growth – Jingjing Wang – Scientific Reports

MALDI-TOF: Investigation of the interactions between Chrysanthemum morifolium flowers extract and intestinal bacteria from human and rat – Jin-hua Tao – Biomedical Chromatography

Substrate-driven convergence of the microbial community in lignocellulose-amended enrichments of gut microflora from the Canadian beaver (Castor canadensis) and North American moose (Alces americanus) – Mabel Ting Wong – Frontiers in Microbiology

Animal microbiome
Epimicrobiota Associated with the Decay and Recovery of Orbicella Corals Exhibiting Dark Spot Syndrome – Julie L. Meyer – Frontiers in Microbiology

Plant, root, and soil microbiome

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics – Nicholas A. Bokulich – mBio

Archaeal Community Changes Associated with Cultivation of Amazon Forest Soil with Oil Palm – Daiva Domenech Tupinambá – Archaea

Effects of Frangula alnus on soil microbial communities and biogeochemical processes in Wisconsin forests – Joel P. Stokdyk – Plant and Soil

Species-specific effects of plant invasions on activity, biomass, and composition of soil microbial communities – Anna M. Stefanowicz – Biology and Fertility of Soils

Water and extremophile microbiome

Review: Biofilms on glacial surfaces: hotspots for biological activity – Heidi J Smith – NPJ Biofilms and Microbiomes

Press: MSU doctoral student publishes research on microbial biofilms and carbon cycling on glacial surfaces – Montana State University

Diversity of culturable bacteria recovered from Pico Bolívar’s glacial and subglacial environments, at 4,950 m, in Venezuelan Tropical Andes – Johnma Rondón – Canadian Journal of Microbiology

Large differences in bacterial community composition among three nearby extreme waterbodies of the high Andean plateau – Pablo Aguilar – Frontiers in Microbiology

The Vertical Distribution of Sediment Archaeal Community in the “Black Bloom” Disturbing Zhushan Bay of Lake Taihu – Xianfang Fan – Archaea

Built environment microbiome / food microbiology

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community – Stephan Thies – Scientific Reports

Characterization of specific spoilage organisms (SSOs) in vacuum-packed ham by culture-plating techniques and MiSeq next-generation sequencing technologies – Agnieszka Piotrowska-Cyplik – Journal of the Science of Food and Agriculture

Metagenomics and bioinformatics

Linking comparative genomics and environmental distribution patterns of microbial populations through metagenomics – Tom O Delmont – bioRxiv

Species–function relationships shape ecological properties of the human gut microbiome – Sara Vieira-Silva – Nature Microbiology

Press: Unraveling the food web in your gut – The Flanders Institute for Biotechnology – EurekAlert

Protocol: A Brief Review on the Ecological Network Analysis with Applications in the Emerging Medical Ecology – Zhanshan (Sam) Ma – Part of the series Springer Protocols Handbook

Review: The evolution of genome mining in microbes – a review – Nadine Ziemert – Natural Product Reports

Transcriptomics, metabolomics

Integrative analysis of transcriptomic and metabolomic data via sparse canonical correlation analysis with incorporation of biological information – Sandra E. Safo – arXiv

More microbiology

Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity – Emanuele Bosi – PNAS

Microbes in the news

Bill Gates, Jennifer Doudna Will Take Podium at ASM Microbe – Ingrid Hein – Medscape

Insights into the ecology of the microbiome: dynamics of the gut, mouth and skin microbiomes of healthy subjects – Science Daily

Podcast: Profile Of A Scientist: Personalized Medicine, Gut Microbes And The Biology Of Space Travel, with Stanford biologist Mike Snyder – WBUR

WPI students may have discovered three new viruses in Worcester soil – Michael D. Kane – MassLive

Electronic sensor that tells dead bacteria from live by measuring ‘osmoregulation’ is potential future tool for medicine and food safety – Purdue University

Oral microbiome rich environment for study, product development, event attendees told – Hank Schultz – Nutraingredients

Take Care of Your Microbiome and Your Microbiome Will Take Care of You – Aaron M. Renn – Urbanophile

Science, publishing, and career

How to make your article easy to review – Part 4 – 25 tips from experienced reviewers on what to look out for before submitting your article – Elsevier

June 10, 2016

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Volunteers taking ETEC, 3 new E. coli phages, oral microbiomes of cats and dogs, skin microbes in Japanese amphibians, fungi and bacteria in floor dust.

Human oral microbiome

The oral microbiome of patients with axial spondyloarthritis compared to healthy individuals – Jordan E. Bisanz – PeerJ

Human vaginal microbiome

Association of Sexual Debut in Adolescents With Microbiota and Inflammatory Markers – Jespers, Vicky – Obstetrics & Gynecology

Human blood ‘microbiome’

Rapid identification of fungi in culture-negative clinical blood and respiratory samples by DNA sequence analyses – Farida Sidiq – BMC Research Notes

Human gut microbiome

Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment – Mihai Pop – BMC Genomics

Mucosa-Associated Ileal Microbiota in New-Onset Pediatric Crohn’s Disease – Assa, Amit – Inflammatory Bowel Diseases

Three New Escherichia coli Phages from the Human Gut Show Promising Potential for Phage Therapy – Marion Dalmasso – PLOS ONE

“Free living females” sounded… weird. Soluble Corn Fiber Increases Calcium Absorption Associated with Shifts in the Gut Microbiome: A Randomized Dose-Response Trial in Free-Living Pubertal Females – Corrie M Whisner – Journal of Nutrition

Similar Fecal Microbiota Signatures in Patients With Diarrhea-predominant Irritable Bowel Syndrome and Patients With Depression – Yixuan Liu – Clinical Gastroenterology and Hepatology

DGGE: Differences in the Biodiversity of the Fecal Microbiota of Infants With Rotaviral Diarrhea and Healthy Infants – Peng Fei – Jundishapur Journal of Microbiology

Opinion: How Our Other Genome Controls Our Epi-Genome – Antonella Celluzzi – Trends in Microbiology

Review: The role of the gut microbiota in NAFLD – Christopher Leung – Nature Reviews Gastroenterology & Hepatology

Animal microbiome

Diet may influence the oral microbiome composition in cats – Christina J. Adler – Microbiome

Characterising the Canine Oral Microbiome by Direct Sequencing of Reverse-Transcribed rRNA Molecules – James E. McDonald – PLOS ONE

Bacterial microbiomes from vertically-transmitted fungal inocula of the leaf-cutting ant Atta texana – Lucas A. Meirelles – Environmental Microbiology Reports

Defensive insect symbiont leads to cascading extinctions and community collapse – Dirk Sanders – Ecology Letters

Plant, root, and soil microbiome

Subalpine conifers in two different geographic locations host highly similar foliar bacterial endophyte communities – Alyssa A. Carrell – FEMS Microbiology Ecology

Effect of plant growth-promoting bacteria on the growth and fructan production of Agave americana L. – Neyser De La Torre-Ruiz – Brazilian Journal of Microbiology

Composition of the Cutaneous Bacterial Community in Japanese Amphibians: Effects of Captivity, Host Species, and Body Region – Joana Sabino-Pinto – Microbial Ecology

Water and extremophile microbiome

Benthic protists: the under-charted majority – Dominik Forster – FEMS Microbiology Ecology

Methane release from sediment seeps to the atmosphere is counteracted by highly active Methylococcaceae in the water column of deep oligotrophic Lake Constance – Maren Bornemann – FEMS Microbiology Ecology

Review: How mutualisms arise in phytoplankton communities: building eco-evolutionary principles for aquatic microbes – Elena Kazamia – Ecology Letters

Review: All ecosystems potentially host electrogenic bacteria – Nicolas Chabert – Bioelectrochemistry

Pollution and waste and bioreactor microbiology

Arsenic metabolism and toxicity influenced by ferric iron in simulated gastrointestinal tract and the roles of gut microbiota – Haiyan Yu – Environmental Science & Technology

Pyrosequencing analysis of bacterial diversity in soils contaminated long-term with PAHs and heavy metals: Implications to bioremediation – Saranya Kuppusamy – Journal of Hazardous Materials

A strange combination of samples: Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies – Simon Güllert – Biotechnology for Biofuels

Monitoring the impact of bioaugmentation with a PAH-degrading strain on different soil microbiomes using pyrosequencing – S. Festa – FEMS Microbiology Ecology

Built environment microbiome

Fungal and bacterial growth in floor dust at elevated relative humidity levels – Karen C. Dannemiller – Indoor Air

Bioinformatics and statistics

An Introduction to Programming for Bioscientists: A Python-Based Primer – Berk Ekmekci – PLOS Computational Biology

Ten Simple Rules for Effective Statistical Practice – Robert E. Kass – PLOS Computational Biology

Bipartite Graphs for Visualization Analysis of Microbiome Data – Karel Sedlar – Evolutionary Bioinformatics

Techniques

The source of SYBR green master mix determines outcome of nucleic acid amplification reactions – Jianxin Yang – BMC Research Notes

More microbiology

Ancestral Tryptophan Synthase Reveals Functional Sophistication of Primordial Enzyme Complexes – Florian Busch – Cell Chemical Biology

Press: Ancient enzyme resurrected from the ancestor of all bacteria – Conor Gearin – New Scientist
Bacteria perfected protein complexes more than 3.5 billion years ago – Science Daily

Microbes in the news

Tufts microbiologist Cecilia A. Silva-Valenzuela, Ph.D., named Pew Latin American Fellow
Silva-Valenzuela, in Andrew Camilli’s lab, will investigate novel approaches to prevent cholera outbreaks – EurekAlert

Bio-statistician Albert Parker with MSU’s Center for Biofilm Engineering earns top EPA award – Amanda Eggert – Montana State University

Video series with James Hamblin – The Atlantic
Should You Map Your Microbiome? A visit to uBiome
Your Probiotics Aren’t Doing Anything (Yet)
You Probably Don’t Need to Shower – James Hamblin – The Atlantic

Banking on stool despite an uncertain future – Tina Amirtha – Science

Science, publishing, and career

In effort to understand continuing racial disparities, NIH to test for bias in study sections – Jeffrey Mervis – Science

Triplicated paper with multiplicated cells and images – Leonid Schneider – For Better Science
Author denies accusations of blatant duplication – Shannon Palus – Retraction Watch

Bik’s Picks (it’s not microbiology, but pretty cool)

RhizoTubes as a new tool for high throughput imaging of plant root development and architecture: test, comparison with pot grown plants and validation – Christian Jeudy – Plant Methods

June 9, 2016

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Salivary microbiome in Behcet’s disease, microbial RNA in human blood, acetate implied in metabolic syndrome, effects of fire retardant on plant–microbe interactions, and a book about the marine microbiome.

Events

ASM Microbe TweetUp: Friday June 17, 11.45-12:30, in the Peer-to-Peer Exchange Zone (in the Exhibition Hall)

Focused meeting: Molecular Biology of Archaea 5, London, UK, 1-3 August 2016

Pregnancy and birth

Infant Early Gut Colonization by Lachnospiraceae: High Frequency of Ruminococcus gnavus – Valeria Sagheddu – Frontiers in Pediatrics

Review: The microbiome during pregnancy and early postnatal life – Josef Neu – Seminars in Fetal and Neonatal Medicine

Review: The human milk microbiome and factors influencing its composition and activity – Carlos Gomez-Gallego – Seminars in Fetal and Neonatal Medicine

Human blood microbiome

Total RNA Sequencing reveals microbial communities in human blood and disease specific effects – Serghei Mangul – bioRxiv

Human mouth microbiome

A Study of the Variation in the Salivary Peptide Profiles of Young Healthy Adults Acquired Using MALDI-TOF MS – Andrei Prodan – PLOS ONE

Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet’s disease – Patrick Coit – Clinical Immunology

Human gut microbiome

Review: What’s bugging your teen? —The microbiota and adolescent mental health – Karen-Anne McVey Neufeld – Neuroscience & Biobehavioral Reviews

Bio-banking gut microbiome samples – Shankar Bolan – EMBO Reports

Animal experiments

Acetate mediates a microbiome–brain–β-cell axis to promote metabolic syndrome – Rachel J. Perry – Nature

Press: How altered gut microbes cause obesity – Science Daily
Fecal Transplant Shows Gut Microbes Cause Obesity – In Rats, Anyway – Science 2.0

Sex-specific Effects of Arsenic Exposure on the Trajectory and Function of the Gut Microbiome – Liang Chi – Chemical Research in Toxicology

Taxonomic assessment of rumen microbiota using total RNA and targeted amplicon sequencing approaches – Fuyong Li – Frontiers in Microbiology

Environmental filtering decreases with fish development for the assembly of gut microbiota – Qingyun Yan – Environmental Microbiology

Animal microbiome

Bacterial Community Diversity Harboured by Interacting Species – Mikaël Bili – PLOS ONE

Plant, root, and soil microbiome

Cascading effects of fire retardant on plant–microbe interactions, community composition, and invasion – Abigail Marshall – Ecological Applications

Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration – Charlotte J. Alster – Journal of Geophysical Research

Selection and evaluation of microorganisms for biocontrol of Verticillium dahliae in olive – A Varo – Journal of Applied Microbiology

Influence of plant genotype on the cultivable fungi associated to tomato rhizosphere and roots in different soils – Anna Poli – Fungal Biology

Arbuscular mycorrhizal fungal communities in buffelgrass pasture under intercropping and shading systems in Brazilian semiarid conditions – Karen M.S. Menezes – Agriculture, Ecosystems & Environment

Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression – Adam J. Book – PLOS Biology

Press: Chemistry lessons from bacteria may improve biofuel production – Science Daily

Review: Streptomyces as a plant’s best friend? – Tom Viaene – FEMS Microbiology Ecology

Water and extremophile microbiome

Light availability regulates the response of algae and heterotrophic bacteria to elevated nutrient levels and warming in a northern boreal peatland – Lily Y. Gu – Freshwater Biology

Metagenomic covariation along densely sampled environmental gradients in the Red Sea – Luke R Thompson – bioRxiv

Microbial community structure of Arctic seawater as revealed by pyrosequencing – Yang Li – Acta Oceanologica Sinica

A snapshot on spatial and vertical distribution of bacterial communities in the eastern Indian Ocean – Jing Wang – Acta Oceanologica Sinica

Pond Crash Forensics: Presumptive identification of pond crash agents by next generation sequencing in replicate raceway mass cultures of Nannochloropsis salina – Laura T. Carney – Algal Research

Detection of antibiotic-resistant bacteria endowed with antimicrobial activity from a freshwater lake and their phylogenetic affiliation – Zothanpuia – PeerJ

Microbial diversity in lake–river ecotone of Poyang Lake, China – Xiaolan Huang – Environmental Earth Sciences

Book: The Marine Microbiome. An Untapped Source of Biodiversity and Biotechnological Potential – Lucal J. Stal, Mariana Silvia Cretoiu – Springer

Food microbiology

Bacterial dynamics and functional analysis of microbial metagenomes during ripening of Dutch-type cheese – Davide Porcellato – International Dairy Journal

Pollution and waste microbiology

Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters – Daniel Carey – Environ Sci Processes Impacts

Computational models of microbiome research, bioinformatics

Synergistic elimination of bacteria by phage and the immune system – Chung Yin (Joey) Leung – bioRxiv

A new way to publish metagenomics studies – Folker Meyer – BioMed Central

Techniques

RNA-stable isotope probing: from carbon flow within key microbiota to targeted transcriptomes – Tillmann Lueders – Current Opinion in Biotechnology

More microbiology

Centenary of the death of Elie Metchnikoff: A visionary and an outstanding team leader –
Jean-Marc Cavaillon – Microbes and Infection

Microbes in the news

Worcester Polytechnic Institute Students Isolate Potentially Novel Soil-Dwelling Viruses – PR Web

Yuck factor may boost hand hygiene compliance: Interview with Ashley Gregory – EurekAlert

Europe orders Italians to cut down olive trees infected with bacteria – Nick Squires – The Telegraph

It’s Not Just Restaurants—Scientists Are Fascinated With Fermented Foods Too – Jane Lear – Take Part

Science, publishing, and career

Differences in incomes of physicians in the United States by race and sex: observational study – Dan P. Ly – British Medical Journal

Press: White male doctors earn 35 percent more than black male doctors – Jennifer Adaeze Okwerekwu – STAT News

June 6, 2016

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Human oral microbiome

Identification of oral bacteria on titanium implant surfaces by 16S rDNA sequencing – Fabiana de Melo – Clinical Oral Implants Research

Subgingival microbiota in individuals with severe chronic periodontitis – Chi-Ying Tsai – Journal of Microbiology, Immunology and Infection

Human gut microbiome

Gut to brain interaction in Autism Spectrum Disorders: a randomized controlled trial on the role of probiotics on clinical, biochemical and neurophysiological parameters – Elisa Santocchi – BMC Psychiatry

Review: Resource conflict and cooperation between human host and gut microbiota: implications for nutrition and health – Helen Wasielewski – Annals of the New York Academy of Sciences

Press: War and peace in the human gut: probing the microbiome -Biodesign

Animal and tissue culture experiments

Adult microbiota-deficient mice have distinct dendritic morphological changes: differential effects in the amygdala and hippocampus – Pauline Luczynski – European Journal of Neuroscience

Exposure to common respiratory bacteria alters the airway epithelial response to subsequent viral infection – Carla Bellinghausen – Respiratory Research

Animal microbiome

Gut microbiota of Busseola fusca (Lepidoptera: Noctuidae) – Maxi Snyman – World Journal of Microbiology and Biotechnology

Plant, root, and soil microbiome

The interconnected rhizosphere: High network complexity dominates rhizosphere assemblages – Shengjing Shi – Ecology Letters

Functional Role of Bacteria from Invasive Phragmites australis in Promotion of Host Growth – M. A. Soares – Microbial Ecology

Design defines the effects of nanoceria at a low dose on soil microbiota and the potentiation of impacts by canola plant – Mohamed Hamidat – Environmental Science & Technology

Water and extremophile microbiome

Taxon interactions control the distributions of cryoconite bacteria colonizing a High Arctic ice cap – Jarishma K. Gokul – Molecular Ecology

Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic – Sunil Mundra – MicrobiologyOpen

Microbial sedimentary imprint on the deep Dead Sea sediment – Camille Thomas – The Depositional Record

Characterization of the cyanobacteria and associated bacterial community from an ephemeral wetland in New Zealand – Nick H. Secker – Journal of Phycology

Abundance of sulfur-degrading bacteria in a benthic bacterial community of shallow sea sediment in the off-Terengganu coast of the South China Sea – Zahar Marziah – MicrobiologyOpen

Pollution and waste microbiology

Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing – Lei Wang – Marine Pollution Bulletin

Effects of erythromycin, trimethoprim and clindamycin on attached microbial communities from an effluent dominated prairie stream – M.J. Waiser – Ecotoxicology and Environmental Safety

Metagenomics and bioinformatics

MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data – Vladimir I. Ulyantsev – Bioinformatics

MDSINE: Microbial Dynamical Systems INference Engine for microbiome time-series analyses – Vanni Bucci – Genome Biology

Microbes in the news

New Bacterial Research May Help Reduce Excessive Amounts Of Phosphorus In Lakes –
Catherine Cabral-Isabedra – Tech Times

About Nicholas Muzyczka, microbiology professor at the University of Florida: Inventor says fame is fine, but best reward is helping others – Anthony Clark – Gainesville.com

Bacteria has potential to clean up oil spills – Zia Lyle – Daily Texan Online

Clif Bars join list of products recalled over listeria concern – Debra Goldschmidt – CNN

Microbes in Space: JPL Researcher Explores Tiny Life – NASA

Jason Tetro aims to rehabilitate microbes’ bad reputation with The Germ Files – Rebecca Tucker – National Post

Science, publishing, and career

Publishing for academic refugees: Paul Ostwald: The Journal of Interrupted Studies – Emma Christie – Oxford Student

Postdoc mysteries: three recent developments raise puzzling uncertainties about postdocs’ present and future lives – Beryl Lieff Benderly – Science

June 2, 2016

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Neck radiation and oral pathogen increase, menopause and the vaginal microbiome, nectar microbes, raw camel milk, and a review on short-chain fatty acids.

Human skin microbiome

Review: Microbial Ecology of the Human Skin – Anthony M. Cundell – Microbial Ecology

Human oral microbiome

Head and neck intensity modulated radiation therapy leads to an increase of opportunistic oral pathogens – Jennifer M. Schuurhuis – Oral Oncology

Human respiratory microbiome

Airway Microbiota Determines Innate Cell Inflammatory or Tissue Remodeling Profiles in Lung Transplantation – Eric Bernasconi – American Journal of Respiratory and Critical Care Medicine

Human vaginal microbiome

Review: Menopause and the Vaginal Microbiome – Alicia L. Muhleisen – Maturitas

Human gut microbiome

Not sure why this got published in Neurocomputing, also very poor English:
Gut microbiota community adaption during young children fecal microbiota transplantation by 16s rDNA sequencing – Jian-Lei Gu – Neurocomputing

Commentary: Transkingdom interactions: Liver flukes and the microbiota in cancer – Lisa Osborne – EBioMedicine

Review: Complex Relationships Between Food, Diet, and the Microbiome – Laura A. Pace – Gastroenterology Clinics of North America

Animal microbiome

Caribbean corals house shared and host-specific microbial symbionts over time and space – Nathaniel D. Chu – Environmental Microbiology Reports

Genome evolution and nitrogen-fixation in bacterial ectosymbionts of a protist inhabiting wood-feeding cockroaches – Vera Tai – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Nectar microbes can reduce secondary metabolites in nectar and alter effects on nectar consumption by pollinators – Rachel L. Vannette – Ecology

The Root-Associated Microbial Community of the World’s Highest Growing Vascular Plants – Roey Angel – Microbial Ecology

Plant community and soil chemistry responses to long-term nitrogen inputs drive changes in alpine bacterial communities – Xia Yuan – Ecology

Forest composition modifies litter dynamics and decomposition in regenerating tropical dry forest – Erik M. Schilling – Oecologia

Metal contamination status of the soil-plant system and effects on the soil microbial community near a rare metal recycling smelter – Zhu Li – Environmental Science and Pollution Research

Tree species, spatial heterogeneity, and seasonality drive soil fungal abundance, richness, and composition in Neotropical rainforests – Stephanie N. Kivlin – Environmental Microbiology

Review: Emerging Insights on Brazilian Pepper Tree (Schinus terebinthifolius) Invasion: The Potential Role of Soil Microorganisms – Karim Dawkins – Frontiers in Plant Science

Food microbiology

Bacteriological quality of raw camel milk along the market value chain in Fafen zone, Ethiopian Somali regional state – Tsegalem Abera – BMC Research Notes

Bioreactor microbiology

Comparison of microbial communities of activated sludge and membrane biofilm in 10 full-scale membrane bioreactors – Sung Jun Jo – Water Research

Phages and viruses

Phagonaute: A web-based interface for phage synteny browsing and protein function prediction – Hadrien Delattre – Virology

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes – Branko Rihtman – PeerJ

Metagenomics and bioinformatics

Identification and analysis of integrons and cassette arrays in bacterial genomes – Jean Cury – Nucleic Acids Research

Uncovering oral Neisseria tropism and persistence using metagenomic sequencing – Claudio Donati – Nature Microbiology

Improved metagenome screening efficiency by random insertion of T7 promoters – Yu Jung Kim – Journal of Biotechnology

Experiences in integrated data and research object publishing using GigaDB – Scott C Edmunds – International Journal on Digital Libraries

Techniques

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples – Satyabrata Bag – Scientific Reports

Proteomics, metabolomics

In vitro metabolic labeling of intestinal microbiota for quantitative metaproteomics – Xu Zhang – Analytical Chemistry

Syntrophic metabolism of vitamins and amino acids in gut microbial community as revealed by in silico genomic analyses – Matvei Sergeevich Khoroshkin – The FASEB Journal

Review: From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites – Ara Koh – Cell

More microbiology

Survey of laboratory-acquired infections around the world in biosafety level 3 and 4 laboratories – N. Wurtz – European Journal of Clinical Microbiology & Infectious Diseases

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

Perspective: Cooperative Microbial Tolerance Behaviors in Host-Microbiota Mutualism – Janelle S. Ayres – Cell

Review: Multifaceted Interfaces of Bacterial Competition – Reed M. Stubbendieck – Journal of Bacteriology

Microbes in the news

Featuring our former lab member Kate Rubins: Napa native heading to International Space Station on 1st space mission – ABC7news

American Gut Project Expands to Asia – Crowdsourced microbiome sequencing effort seeks participant diversity – Heather Buschman – UC San Diego Health

Making sense of microbiomes – UCI biochemist studies the effect of unique virus, bacteria and fungi on kids’ health – Tom Vasich – UCI News

11 deaths at Huntington Hospital among patients infected by dirty scopes, city report says – LA Times
Deadly dirty medical scopes still threaten trusting patients – My News LA

Walnuts may improve your colon health: Eating walnuts changes the gut microbiome and reduces cancer growth – EurekAlert

Gluten-Free Diet Induces Changes In Gut Microbiome – Interview with Ettje Tigchelaar – Medical Research

Fecal Transplants Effective for Healing Ulcerative Colitis – HCP Live

Gut Microbiome Tied to Metabolic Hormones in Early Pregnancy – Doctors Lounge

Human Gut Microbiome May Help Identify New Ways of Preventing and Treating Diabetes – Endocrinology Advisor

Researchers poo poo antibiotics – Vet Practice Magazine

Video: Susannah Tringe talks about metagenomics analysis tools and the challenges of gaining a systems-level understanding of a microbial community – Vizbi

Cold shock: E.coli bacteria found in 92 per cent ice samples in Mumbai – MidDay

Science, publishing, and career

The scientist’s guide to summer reading – Science

What does scientific reproducibility mean, anyway? – Ivan Oransky and Adam Marcus – STAT News