Category Archives: Archaea

September 29, 2016

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Two human skin microbiota papers, effects of eating chili powder, methanogens can tolerate Mars-like low pressure, gut microbiota signatures of longevity.

Human skin microbiome

Topical Decolonization Does Not Eradicate the Skin Microbiota of Community-Dwelling or Hospitalized Adults – Carey-Ann D. Burnham – Antimicrobial Agents and Chemotherapy

Evolutionary and Functional Implications of Hypervariable Loci Within the Skin Virome – Geoffrey D Hannigan – bioRxiv

Human gut microbiome

Healthy subjects differentially respond to dietary capsaicin correlating with the specific gut enterotypes – Chao Kang – Journal of Clinical Endocrinology & Metabolism

Gut microbiota signatures of longevity – Fanli Kong – Current Biology

Shifts in the fecal microbiota associated with adenomatous polyps – Vanessa L Hale – Cancer Epidemiology, Biomarkers & Prevention

When pathogenic bacteria meet the intestinal microbiota – Nathalie Rolhion – Philosophical Transactions of the Royal Society B

Review: From homeostasis to pathology: decrypting microbe–host symbiotic signals in the intestinal crypt – Thierry Pédron – Philosophical Transactions of the Royal Society B

Review: Human microbiome as therapeutic intervention target to reduce cardiovascular disease risk – Annefleur M. Koopen – Current Opinion in Lipidology

Review: The microbial epigenome in metabolic syndrome – Marlene Remely – Molecular Aspects of Medicine

Animal and in vitro models

Probiotic legacy effects on gut microbial assembly in tilapia larvae – Christos Giatsis – Scientific Reports

D-Tryptophan from probiotic bacteria influences the gut microbiome and allergic airway disease – Inge Kepert – The Journal of Allergy and Clinical Immunology

Expression of the aryl hydrocarbon receptor contributes to the establishment of intestinal microbial community structure in mice – Iain A. Murray – Scientific Reports

Animal microbiome

The chicken tracheal microbiome: unexpected preliminary data – Tim Johnson Lab

Contrasting diets reveal metabolic plasticity in the tree-killing beetle, Anoplophora glabripennis (Cerambycidae: Lamiinae) – Charles J. Mason – Scientific Reports

Plant, root, and soil microbiome

Structure, Variation, and Co-occurrence of Soil Microbial Communities in Abandoned Sites of a Rare Earth Elements Mine – Yuanqing Chao – Environmental Science & Technology

Fungal endophytes as priority colonizers initiating wood decomposition – Zewei Song – Functional Ecology

Water and extremophile microbiome

Culture-independent study of bacterial communities in tropical river sediment  –
Honglada Thoetkiattikul – Bioscience, Biotechnology, and Biochemistry

Oligotrophic lagoons of the South Pacific Ocean are home to a surprising number of novel eukaryotic microorganisms – Eunsoo Kim – Environmental Microbiology

Low Pressure Tolerance by Methanogens in an Aqueous Environment: Implications for Subsurface Life on Mars – R. L. Mickol – Origins of Life and Evolution of Biospheres

Microbes and robots

Did not quite grasp the abstract, but cool picture of a small robot: Bioinspired decision architectures containing host and microbiome processing units – K C Heyde – Bioinspiration & Biomimetics

Microbes in the news
Research Breakthrough Could Help Diagnose, Treat Biofilm Infections – Lorena Anderson – UC Merced

Profile: Dr. Bonnie Bassler, a pioneer who’s investigating how bacteria communicate – Joe Tyrrell – New Jersey Spotlight

World’s Largest MS Research Conference Highlights Advances in Progressive MS, Gut Microbiome, Managing Symptoms, and New Approaches to Restoring Function – National MS Society

Assembly Biosciences Announces Key Additions to Microbiome Team – Globe Newswire

Can’t lose weight? You might be able to blame it on your parents—and their gut bacteria – Akshat Rathi – Quartz
Are Your Genes Making It Hard To Get Into Your Jeans? – Julie Taylor – uBiome blog

Deadly Mud-Dwelling Bacteria Melioidosis Stirs In The Northern Territory – Cayla Dengate – Huffington Post Australia

 

Science, publishing, and career

Young researchers thrive in life after academia. Alternative career paths should be celebrated, not seen as a compromise. – Nature

June 18, 2016

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Your Saturday Microbiome Digest: CSF metagenomics in multiple sclerosis, Caenorhabditis elegans responses to bacteria, and archaeal communities in permafrost.

Infection and microbes

Only microbial contamination found: Metagenomic Analysis of Cerebrospinal Fluid from Patients with Multiple Sclerosis – Karol Perlejewski – Advances in Experimental Medicine and Biology

Review: The regulation of host defences to infection by the microbiota – Rebecca L. Brown – Immunology

Animal and in vitro experiments

Microbial Community Transplant Results in Increased and Long-Term Oxalate Degradation – Aaron W. Miller – Microbial Ecology

Differential Utilization of Basic Proline-Rich Glycoproteins During Growth of Oral Bacteria in Saliva – Yuan Zhou – Applied and Environmental Microbiology

Caenorhabditis elegans responses to bacteria from its natural habitats – Buck S. Samuel – PNAS

Plant, root, and soil microbiome

Presence and persistence of viable, clinically relevant Legionella pneumophila bacteria in garden soil in the Netherlands – E. van Heijnsbergen – Applied and Environmental Microbiology

Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons – C. Ryan Pento – Frontiers in Microbiology

Monitoring fungi in ecological restorations of coastal Indiana, U.S.A. – Peter G. Avis – Restoration Ecology

Review: Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing “Stress-on-Stress” Responses – Hamed Azarbad – MDPI International Journal of Molecular Sciences

Water and extremophile microbiome

Archaeal communities of Arctic methane-containing permafrost – Victoria Shcherbakova – FEMS Microbiology Ecology

Microbial community diversity, structure, and assembly across oxygen gradients in meromictic marine lakes, Palau – Matthew S. Meyerhof – Environmental Microbiology

Bioreactor microbiology

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant – Vera Ortseifen – Journal of Biotechnology

Bioinformatics

Finds microbial interactions based on PubMed abstracts, so basically finding interactions that were already published (???): @MInter: Automated Text-mining of Microbial Interactions – Lim Kun Ming Kenneth – Bioinformatics

More microbiology

In situ replication rates for uncultivated bacteria in microbial communities – Christopher T Brown – bioRxiv

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities – Sebastian Germerodt – PLOS Computational Biology

Microbes in the news

UWM professor taking a deeper dive on beach pollution data – Milwaukee-Wisconsin Journal Sentinel

The medical revolution that delves into humans’ inner aliens – Robert Matthews – The National

Brewing on the wild side: IU’s Dr. Matthew L. Bochman – Rita Kohn – Nuvo.net

Fecal bacteria and antibiotic resistance genes found in water samples from fly-in Northern Manitoba – Ian Graham – Thompson Citizen

CosmosID, BioCollective Collaborate on Microbiome Analysis Kit – GenomeWeb

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 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 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

May 21, 2016

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Helminths positively associated with allergy, baboon vaginal microbiome, nitrogen fixation in poplar trees, boreal lakes as analogues for the Archaean ocean, and PERMANOVA-S as alternative for weighted Unifrac.

Events

2016 Society for Industrial Microbiology and Biotechnology (SIMB) Annual Meeting and Exhibition – July 24-30, New Orleans, LA

General
Editorial overview: Remapping the body of the world: Exploring interactions at the interface of microbial ecology, biological engineering and information science – Steven J. Hallam – Current Opinion in Microbiology

Human oral microbiome

Quantitative molecular detection of 19 major pathogens in the interdental biofilm of periodontally healthy young adults – Florence Carrouel – Frontiers in Microbiology

Species level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population – Nezar Noor Al-hebshi – Journal of Oral Microbiology

Review: Metagenomic Insights into Transferable Antibiotic Resistance in Oral Bacteria – S. Sukumar – Journal of Dental Research

Human gut microbiome

Helminths are positively associated with atopy and wheeze in Ugandan fishing communities: results from a cross-sectional survey – E. L. Webb – Allergy

Stool frequency is associated with gut microbiota composition – Fatemeh Hadizadeh – Gut

The gut-adherent microbiota of PSC–IBD is distinct to that of IBD – Mohammed Nabil Quraishi – Gut

Mucosal adherent bacterial dysbiosis in patients with colorectal adenomas– Yingying Lu – Scientific Reports

Haloferax massiliensis sp. nov., the first human-associated halophilic archaea – Saber Khelaifia – New Microbes and New Infections

Review: The influence of commensal and pathogenic gut microbiota on prion disease pathogenesis – David S. Donaldson – Journal of General Virology

Animal experiments

Effect of Dietary Fibers on Cecal Microbiota and Intestinal Tumorigenesis in Azoxymethane Treated A/J Min/+ Mice – Birgitte Moen – PLOS ONE

Food-grade antimicrobial ɛ-polylysine transiently perturbs the structure of the murine gut microbiome – Xiaomeng You – The FASEB Journal

Animal microbiome

Baboon vaginal microbial flora – Jael A. Obiero – Journal of Medical Primatology

Diversity and fluctuation in ciliate protozoan population in the rumen of cattle – Arfan Abrar – Animal Science Journal

Dietary-driven variation effects on the symbiotic flagellate protist communities of the subterranean termite Reticulitermes grassei Clément – S. Duarte – Journal of Applied Entomology

Plant, root, and soil microbiome

Variable Nitrogen Fixation in Wild Populus – Sharon L. Doty – PLOS ONE

Press: Bacteria in branches naturally fertilize trees – Michelle Ma – University of Washington

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database – Andrew Bissett – GigaScience

Conference abstract: Microbial communities associated with the biotransformation potential of insensitive explosives in surface soils – F. Crocker – 2016 SIMB Annual Meeting and Exhibition

Water and extremophile microbiome

Millions of Boreal Shield Lakes can be used to Probe the Evolution of Archaean Ocean Life – Sherry Schiff – bioRxiv

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution – Beatriz Díez – PLOS ONE

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

Biogeography of sulfur-oxidizing Acidithiobacillus populations in extremely acidic cave biofilms – Daniel S Jones – ISME Journal

Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage – Sara Billerbeck – Nature Microbiology

Drinking water, waste and pollution microbiology

Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions – Yingyu Law – Scientific Reports

Conference abstract: Microbial survival in drinking water systems – A. Pinto – 2016 SIMB Annual Meeting and Exhibition

Bioinformatics

PERMANOVA-S: Association test for microbial community composition that accommodates confounders and multiple distances – Zheng-Zheng Tang – Bioinformatics

More microbiology

ppGpp couples transcription to DNA repair in E. coli – Venu Kamarthapu – Science

Press: Factor preserves DNA integrity in bacteria despite assault from antibiotics – Science Daily
Spatial organization shapes the turnover of a bacterial transcriptome – Jeffrey R Moffitt – eLIFE

The Small World Initiative™: An Innovative Crowdsourcing Platform for Antibiotics – Ana Maria Barral – The FASEB Journal

Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities – Yinghua Zha – PLOS ONE

Microbes in the news

Featuring my work (but not my quotes): The inner lives of dolphins – Marine mammals carry an unexpected microbial mix – Steve Fyffe – Stanford Medicine Magazine

About Stanley Falkow and Denise Monack: Microbe mentoring: The recipe for success includes independence, a gentle shove and a good stiff drink – Kathy Zonana – Stanford Medicine Magazine

President Obama Awards the National Medals of Science & Technology and Innovation. Stanford Professor of Microbiology Stanley Falkow get his award at 11:30 min in this video.

Students are developing bacteria that eat plastic polluting our oceans. Om nom. – Josh Hrala – Science Alert

A Comprehensive Survey of Preclinical Microbiology Curricula Among US Medical Schools – Dora J. Melber – Clinical Infectious Diseases

University Of California, San Diego Invests $12 Million In Its Own Microbiome Research Efforts! – Vinny – University Herald

Bik’s Picks

Striking Immune Phenotypes in Gene-Targeted Mice Are Driven by a Copy-Number Variant Originating from a Commercially Available C57BL/6 Strain – Vinay S. Mahajan

Press: Immune Defect Detected in Knockout Mice – Tanya Lewis – The Scientist

May 12, 2016

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Dandruff, archaeological dental calculus methanogens, extreme longevity, UK twins, and dissemination of human-derived bacteria into the Antarctic microbiome.

Pregnancy and birth microbiome

Early-life gut microbiome composition and milk allergy resolution – Supinda Bunyavanich – Journal of Allergy and Clinical Immunology

Human skin microbiome

Dandruff is associated with the conjoined interactions between host and microorganisms – Zhijue Xu – Scientific Reports

Human oral microbiome

Restricted diversity of dental calculus methanogens over five centuries, France – Hong T. T. Huynh – Scientific Reports

Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer – Kaitlin J. Flynn – mSphere

Peri-implant and periodontal microbiome diversity in aggressive periodontitis patients: a pilot study – Vanessa Sousa – Clinical Oral Implants Research

Human respiratory microbiome

The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study – Moana Mika – The Lancet Respiratory Medicine

Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR – Joshua R. Stokell – Antonie van Leeuwenhoek

Human gut microbiome

Gut Microbiota and Extreme Longevity – Elena Biagi – Current Biology

Enteral feeding reduces metabolic activity of the intestinal microbiome in Crohn’s disease: an observational study – C Walton – European Journal of Clinical Nutrition

Genetic Determinants of the Gut Microbiome in UK Twins – Julia K. Goodrich – Cell Host & Microbe

Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study – Christian Milani – Scientific Reports

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing – Emily Vogtmann – PLOS ONE

Review: Structural and functional changes within the gut microbiota and susceptibility to Clostridium difficile infection – Caná L. Ross – Anaerobe

Preview: What’s LPS Got to Do with It? A Role for Gut LPS Variants in Driving Autoimmune and Allergic Disease – Taylor Feehley – Cell Host & Microbe

Review: Koch’s postulates, microbial dysbiosis and inflammatory bowel disease – Benjamin P. Willing – Clinical Microbiology and Infection

Review: Impact of gut microbiota on diabetes mellitus – G. Blandino – Diabetes & Metabolism

Review: Microbiota and the nitrogen cycle: Implications in the development and progression of CVD and CKD – David Briskey – Nitric Oxide

Review: Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract – Jenessa A. Winston – Anaerobe

Review: The microbiome-immune-host defense barrier complex (microimmunosome) and developmental programming of noncommunicable diseases – Rodney R. Dietert – Reproductive Toxicology

Animal experiments

A low dose of an organophosphate insecticide causes dysbiosis and sex-dependent responses in the intestinal microbiota of the Japanese quail (Coturnix japonica) – Eduardo Crisol-Martínez – PeerJ

Structural modulation of gut microbiota by chondroitin sulfate and its oligosaccharide – Qingsen Shang – Macromolecules

Administration of probiotic kefir to mice with Clostridium difficile infection exacerbates disease – Jennifer K. Spinler – Anaerobe

Editorial: Immunology: You Remind Me of a Microbe I Know – Ray Soto and June Round – Current Biology

Forum: Human Microbiota-Associated Mice: A Model with Challenges – Marie-Claire Arrieta – Cell Host & Microbe

Plant, root, and soil microbiome

Geography and agronomical practices drive diversification of the epiphytic mycoflora associated with barley and its malt end product in western Canada – Wen Chen – Agriculture, Ecosystems & Environment
http://www.sciencedirect.com/science/article/pii/S0167880916301669

Revisiting the pink-red pigmented basidiomycete mirror yeast of the phyllosphere –
Alec Cobban – MicrobiologyOpen
http://onlinelibrary.wiley.com/doi/10.1002/mbo3.374/abstract

 

Water and extremophile microbiome

Escherichia coli out in the cold: Dissemination of human-derived bacteria into the Antarctic microbiome – Michelle L. Power – Environmental Pollution

Habitat heterogeneity and connectivity shape microbial communities in South American peatlands – Felix Oloo – Scientific Reports

The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants – Ghada A. Mustafa – Environmental Pollution

Conference Highlight: Decoding Microbial “Relationship Statuses” at OSM 2016 – Kelsey Ellis – Bulletin Limnology and Oceanography

Phages and viruses

Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology – Angela L. Rasmussen – Cell Host & Microbe

Techniques

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface – Pranjul Shah – Nature Communications

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants – Cian J. Hill – Microbiome

Video: Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization – Melis N. Anahtar – JOVE

Microbial Ecology

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments – Scott W. Olesen – PLOS ONE

More microbiology

Self-driven jamming in growing microbial populations – Morgan Delarue – bioRxiv

Review: Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics – Elizabeth Klemm – Cell Host & Microbe

Microbes in the news

Osel, Inc.’s Lead Product LACTIN-V Enters Phase 2b Study to Prevent Recurrence of Bacterial Vaginosis– Digital Journal

Bacteria Battle Can Lead to Dandruff – Jennifer Viegas – Discovery
Bacteria the yin and yang of dandruff, says study – MedicalXpress

New Microbiome Research Tool Offers Potential to Revolutionise Drug Development
– PR Newswire

Experts react to ‘waste of money’ headlines against probiotics – Adi Menayang – NutraIngredients

How scientists are harnessing the ice-making powers of bacteria – Zach St. George – The Week

Researchers Engineer Bacteria to Streamline Biofuel Production Process – IndiaWest

New Microbiome Research Tool Offers Potential to Revolutionise Drug Development – PR Newswire

Twin study finds that gut microbiomes run in families – EurekAlert

From the American Urological Association meeting: Gut Bugs Differ in Chronic Prostatitis. Difference in taxa may aid biomarker, researchers say – MedPageToday

In Infants With Necrotizing Enterocolitis, Gut Dysbiosis Precedes Disease – Julie A. Jacob – JAMA

Science, publishing, and career

Reminder to deposit DNA sequences – Mark Blaxter – Science

Unexpected revelations for study volunteer: What health information do researchers owe the volunteers in their studies – Jennifer Couzin-Frankel – Science

Bik’s Picks

WATCH: What happened to astronaut Scott Kelly’s DNA during his year in space – Carl Zimmer – STAT News

May 3, 2016

Posted on by

Counting the microbial species on Earth, goat rumen microbiome development, red kangaroos who died a tragic death, fungi in burgundy vineyards, Archaea in  Yellowstone, and image irregularities at a Pfizer lab in La Jolla.

Jobs and Events

Postdoctoral Fellowship Opportunity: Microbiology of the Built Environment – Sloan Foundation

Bioinformatics for the Microbiome, May 27 – Stanford Center for Genomics and Personalized Medicine, $49

General microbiology

Scaling laws predict global microbial diversity: Earth is home to as many as 1 trillion (10exp12) microbial species – Kenneth J. Locey – PNAS

Pregnancy and birth

Impact of Prematurity and Perinatal Antibiotics on the Developing Intestinal Microbiota: A Functional Inference Study – Silvia Arboleya – MDPI International Journal of Molecular Sciences

Review: Young microbes for adult obesity – M. Serino – Pediatric Obesity

Review: Microbial therapeutic interventions – Nicole G. Grady – Seminars in Fetal and Neonatal Medicine

Human oral microbiome

Microbiome of Deep Dentinal Caries Lesions in Teeth with Symptomatic Irreversible Pulpitis – Isabela N. Rôças – PLOS ONE

Human respiratory tract microbiome

Nasopharyngeal Microbiota, Host Transcriptome and Disease Severity in Children with Respiratory Syncytial Virus Infection – Wouter A.A. de Steenhuijsen Piters – Am J Respir Crit Care Med.

Human reproductive tract microbiome

Detection of DNA viruses in prostate cancer – Vitaly Smelov – Scientific Reports

Human gut microbiome

Effect of probiotic yoghurt on animal-based diet-induced change in gut microbiota: an open, randomised, parallel-group study – T. Odamaki – Beneficial Microbes

Fecal microbiota transplant for Clostridium difficile infection in older adults – William M. Tauxe – Therapeutic Advances in Gastroenterology

Review: Fine-tuning of the mucosal barrier and metabolic systems using the diet-microbial metabolite axis – Motoyoshi Nagai – International Immunopharmacology

Review: Gut Microbiome in CKD: challenges and opportunities – Anitha Nallu – Translational Research

Editorial: Transplanting a Microbial Organ: the Good, the Bad, and the Unknown – Dionysios A. Antonopoulos – mBio

Animal models
A polyphenol-rich fraction obtained from table grapes decreases adiposity, insulin resistance and markers of inflammation and impacts gut microbiota in high-fat-fed mice – Brian Collins – The Journal of Nutritional Biochemistry

Diet-induced obesity, energy metabolism and gut microbiota in C57BL/6J mice fed Western diets based on lean seafood or lean meat mixtures – Jacob Bak Holm – The Journal of Nutritional Biochemistry

Colonic Inflammation Accompanies An Increase of β-Catenin Signaling and Lachnospiraceae/Streptococcaceae in the Hind Gut of High-Fat Diet-Fed Mice – Huawei Zeng – The FASEB Journal

Gut commensal Bacteroides acidifaciens prevents obesity and improves insulin sensitivity in mice – J-Y Yang – Mucosal Immunology

Composition and Predicted Metabolic Capacity of Upper and Lower Airway Microbiota of Healthy Dogs in Relation to the Fecal Microbiota – Aaron C. Ericsson – PLOS ONE

Cultivation and qPCR Detection of Pathogenic and Antibiotic-Resistant Bacterial Establishment in Naive Broiler Houses – J. P. Brooks – Journal of Environmental Quality

Exploring the Goat Rumen Microbiome from Seven Days to Two Years – Lizhi Wang – PLOS ONE

Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection – Juan J. Quereda – PNAS

Animal microbiome

Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (Macropus rufus) – Meirong Li – World Journal of Microbiology and Biotechnology

Assessment of Bacterial Communities in Thirteen Species of Laboratory-Cultured Domestic Mites (Acari: Acaridida) – Jan Hubert – Journal of Economic Entomology

Bacterial community in Haemaphysalis ticks of domesticated animals from the Orang Asli communities in Malaysia – Jing-Jing Khoo – Ticks and Tick-borne Diseases

Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence – Robert A. Quinn – Proceedings of the Royal Society B

Taxonomic and functional diversity of the culturable microbiomes of epigeic earthworms and their prospects in agriculture – Arjun Singh – Journal of Basic Microbiology

Methanogen Diversity in Indigenous and Introduced Ruminant Species on the Tibetan Plateau – Xiao Dan Huang – Archaea

Horse Species Symposium abstracts: Journal of Animal Science
Recent advances in the microbiome and physiology of the hindgut of the horse and dog – F. Camargo
Canine intestinal microbiology and metagenomics: From phylogeny to function – B. C. Guard – Journal of Animal Science
The microbiome of the horse hindgut: History and current knowledge – V. Julliand

Plant, root, and soil microbiome

Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations – Jincai Ma – Science of the Total Environment

Microbial diversity limits soil heterotrophic respiration and mitigates the respiration response to moisture increase – Fen-Guo Zhang – Soil Biology and Biochemistry

Total and active microbial communities and phoD as affected by phosphate depletion and pH in soil – Sabine A. Ragot – Plant and Soil

Genetically modified WYMV-resistant wheat exerts little influence on rhizosphere microbial communities – Zhenhua Zhang – Applied Soil Ecology

Loss of testate amoeba functional diversity with increasing frost intensity across a continental gradient reduces microbial activity in peatlands – Vincent E.J. Jassey – European Journal of Protistology

Regional-scale analysis of arbuscular mycorrhizal fungi: the case of burgundy vineyards – Marie-Lara Bouffaud – Oeno One

Review: Role of Plant Growth Promoting Rhizobacteria in Agricultural Sustainability—A Review – Pravin Vejan – MDPI Molecules

Chapter: Mycorrhizas in Agroecosystems – Marcela C. Pagano – Recent Advances on Mycorrhizal Fungi

Water and extremophile microbiome

Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water – Maria Aguilar – The Journal of Eukaryotic Microbiology

Drift in ocean currents impacts intergenerational microbial exposure to temperature – Martina A. Doblin – PNAS

Low Genome Content Diversity of Marine Planktonic Thaumarchaeota – Haiwei Luo – Environmental Microbiology Reports

The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park – Zackary J. Jay – Environmental Microbiology

Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water – Carlos Narciso-da-Rocha – Science of the Total Environment

A 150-year record of phytoplankton 1 community succession controlled by hydroclimatic variability in a tropical lake – Kweku Afrifa Yamoah – Biogeosciences

Review: Hydrothermal Vents and Methane Seeps: Rethinking the Sphere of Influence – Lisa A. Levin – Frontiers in Marine Science

Review: Microbial associations with macrobiota in coastal ecosystems: patterns and implications for nitrogen cycling – Orissa M Moulton – Frontiers in Ecology and the Environment

Book: Biotechnology of Extremophile – Springer

Waste and pollution microbiology

Revealing colonisation and biofilm formation of an adherent coal seam associated microbial community on a coal surface – Silas H.W. Vick – International Journal of Coal Geology

Enhanced Degradation of Diesel in the Rhizosphere of Lupinus luteus after Inoculation with Diesel-Degrading and Plant Growth-Promoting Bacterial Strains – María Balseiro-Romero – Journal of Environmental Quality

Built environment microbiology

Urban Microbiomes and Urban Agriculture: What Are the Connections and Why Should We Care? – Gary M. King – Sowing Seeds in the City

Bioinformatics, transcriptomics, metagenomics

rnaQUAST: a quality assessment tool for de novo transcriptome assemblies – Elena Bushmanova – Bioinformatics

Feature: Microbiology: the road to strain-level identification – Vivien Marx – Nature Methods

Protocol Book: Data Mining Techniques for the Life Sciences – Springer
Bacterial Genomic Data Analysis in the Next-Generation Sequencing Era – Massimiliano Orsini
Update on Genomic Databases and Resources at the National Center for Biotechnology Information – Tatiana Tatusova
Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles – Maja Fabijanić

More microbiology

Riches of phenotype computationally extracted from microbial colonies – Tzu-Yu Liu – PNAS

Microbes in the news

UB’s microbiome hunters. These are exciting times at UB as its work on the human genome and microbiome matures. – Research Foundation for The State University of New York

Video: How Your City Has Its Own Unique Microbiome – Discovery News – YouTube

Wrapping up multiple sclerosis at UCSF – Claire Conway – UC San Francisco

Stalking Cave Bacteria to Make Secret Weapons Against Superbugs: Dr. Naowarat Cheeptham – Sam Grobart – Bloomberg

Seres Therapeutics Announces Achievement of Target Enrollment of SER-109 Phase 2 Study for the Prevention of Recurrent Clostridium difficile Infection – Business Wire

Bacteria use traffic-cop-like mechanism to infect gut. WSU scientists discover mechanism critical to pathogens’ success – EurekAlert

Tesla’s Bioweapon Defense Mode can protect you from bacteria, and reduce pollution
Cars. Tesla’s AC unit is available on the Model X and the new Model S – Alphr

Bacteria Hysteria

This odor-fighting, bacteria-killing underwear is made with pure silver – Christian de Looper – Yahoo Digital Trends
Millions of people are drinking mold and bacteria with their coffee. This is how to avoid it! – David Wolfe

Science, publishing and career

Image integrity concerns in papers from a Pfizer lab – Leonid Schneider – For Better Science

May 1, 2016

Posted on by

Events

Bioinformatics for the Microbiome – Stanford Center for Genomics and Personalized Medicine – May 27, 2016

General microbiome

Microbiome sequencing: challenges and opportunities for molecular medicine – Thomas Clavel – Expert Review of Molecular Diagnostics

Human skin microbiome

An In vitro Model for Bacterial Growth on Human Stratum Corneum – Danique A. van der Krieken – Acta Dermato-Venereologica

Human respiratory microbiome

Launching into the Deep: Does the Pulmonary Microbiota Promote Chronic Lung Inflammation and Chronic Obstructive Pulmonary Disease Pathogenesis? – Marc A. Sze – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Targeting the gut to protect the bladder: Oral Phage therapy approaches against urinary Escherichia coli infections? – Harald Brüssow – Environmental Microbiology

Characterization of gut microbiota profiles in coronary artery disease patients using data mining analysis of terminal restriction fragment length polymorphism: gut microbiota could be a diagnostic marker of coronary artery disease – Takuo Emoto – Heart and Vessels

Review: Gut microbiota: an Indicator to Gastrointestinal Tract Diseases – Trupti Patel – Journal of Gastrointestinal Cancer

Review: Gut microbiome and kidney disease: a bidirectional relationship – Souhaila Al Khodor – Pediatric Nephrology

Animal models

Akkermansia Muciniphila Protects Against Atherosclerosis by Preventing Metabolic Endotoxemia-Induced Inflammation in Apoe-/- Mice – Jin Li – Circulation

The effects of maternal and post-weaning diet on gut microbiota and glucose metabolism in mice offspring – Jia Zheng – Bioscience Reports

Effect of Dietary Starch Source and Concentration on Equine Fecal Microbiota – Brittany E. Harlow – PLOS ONE

Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows – Marija Kaevska – Canadian Journal of Microbiology

Molecular exploration of fecal microbiome in quinoa-supplemented obese mice – Jose F. Garcia-Mazcorro – FEMS Microbiology Ecology

Lingonberries alter the gut microbiota and prevent low-grade inflammation in high-fat diet fed mice – Lovisa Heyman-Lindén – Food and Nutrition Research

The influence of fishmeal-free diets on microbial communities in Atlantic salmon Salmo salar recirculation aquaculture systems – Victor Schmidt – Applied and Environmental Microbiology

Insights into the biodiversity of the gut microbiota of broiler chickens – Leonardo Mancabelli – Environmental Microbiology

Maternal exposure to a Western-style diet causes differences in intestinal microbiota composition and gene expression of suckling mouse pups – Wilma T. Steegenga – Molecular Nutrition & Food Research

Animal microbiome

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

Global microbialization of coral reefs – Andreas F. Haas – Nature Microbiology

Comparison of Varroa destructor and Worker Honeybee Microbiota Within Hives Indicates Shared Bacteria – Jan Hubert – Microbial Ecology

Review: Diagnosis and interpretation of intestinal dysbiosis in dogs and cats – Jan Suchodolski – The Veterinary Journal

Plant, root, and soil microbiome

Selective isolation of potentially phosphate-mobilizing, biosurfactant-producing and biodegradative bacteria associated with a sub-Arctic, terricolous lichen, Peltigera membranacea – Margrét Auður Sigurbjörnsdóttir – FEMS Microbiology Ecology

Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites – Frederic Mahe – bioRxiv

Edaphic properties override the influence of crops on the composition of the soil bacterial community in a semiarid agroecosystem – Luke D. Bainard – Applied Soil Ecology

Effects of land use change on the composition of soil microbial communities in a managed subtropical forest – Xiaoping Guo – Forest Ecology and Management

Bioprospecting of Plant Growth Promoting Bacilli and Related Genera Prevalent in Soils of Pristine Sacred Groves: Biochemical and Molecular Approach – Nathaniel A. Lyngwi – PLOS ONE

Aligning molecular studies of mycorrhizal fungal diversity with ecologically important levels of diversity in ecosystems – Ian R Sanders – The ISME Journal

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter – Thea Whitman – The ISME Journal

Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa – I. Moroenyane – Microbial Ecology

Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance – Cécile E. Thion – FEMS Microbiology Ecology

Ecological restoration alters microbial communities in mine tailings profiles – Yang Li – Scientific Reports

Water and extremophile microbiome

Co-occurrence analysis of microbial taxa in the Atlantic Ocean reveals high connectivity in the free-living bacterioplankton – Mathias Milici – Frontiers in Microbiology

Identification of Free-living and Particle-Associated Microbial Communities Present in Hadal regions of the Mariana Trench – Jonathan Tarn – Frontiers in Microbiology

Variation in coastal Antarctic microbial community composition at sub-mesoscale: spatial distance or environmental filtering? – Mario Moreno-Pino – FEMS Microbiology Ecology

Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring – Zhou Jiang – Scientific Reports

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert – J. Goordial – Environmental Microbiology

Built environment microbiome

Melding the Old with the New: Trends in Methods Used to Identify, Monitor, and Control Microorganisms on Cultural Heritage Materials – Patricia Sanmartín – Microbial Ecology

Food microbiology

Overlap of spoilage microbiota between meat and meat processing environment in small-scale vs large-scale retail distribution – Giuseppina Stellato – Applied and Environmental Microbiology

Fermentative capabilities and volatile compounds produced by Kloeckera/Hanseniaspora and Saccharomyces yeast strains in pure and mixed cultures during Agave tequilana juice fermentation – Ivonne Wendolyne González-Robles – Antonie van Leeuwenhoek

Pollution and waste microbiology

The effects of salinity on nitrification using halophilic nitrifiers in a Sequencing Batch Reactor treating hypersaline wastewater – Scientific Reports – You-Wei Cui

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.– Alejandro Palomo – The ISME Journal

Bioinformatics and metagenomics

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2 – Johan Bengtsson-Palme – Ecological Informatics

IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data – Mohamed Mysara – BMC Bioinformatics

Minireview: Tracking strains in the microbiome: insights from metagenomics and models – Ilana L. Brito – Frontiers in Microbiology

Viruses and phages

Review: Endogenized viral sequences in mammals – Nicholas F. Parrish – Current Opinion in Microbiology

Probiotics

Probiotic Cream: Viability of Probiotic Bacteria and Chemical Characterization – Lutfiye Yilmaz-Ersan – Journal of Food Processing and Preservation

Transcriptomics

Use of Metatranscriptomics in Microbiome Research – Stavros Bashiardes – Bioinform Biol Insights

More microbiology

Complex molecular mixtures under cycling gradients as basis for lifes origins – Bert Poolman – bioRxiv

Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’ – Laura Villanueva – Environmental Microbiology

Review: Are you my symbiont? Microbial polymorphic toxins and antimicrobial compounds as honest signals of beneficial symbiotic defensive traits – Kai Hillman – Current Opinion in Microbiology

Microbes in the news

Findings from the Gut—New Insights into the Human Microbiome – Karen Weintraub – Scientific American

What our gut tells us about the ‘hygiene hypothesis’ – Veronica Meade-Kelly – MedicalXpress

Russian scientists prove Antarctic bacteria brought from other continents – TASS

Beer made from belly button fluff has a bit of the brewer in every glass – Jenni Ryal – Mashable @7centBrewery

Yep, This Brewery Makes Beer Using Bacteria From People’s Belly Buttons: “7 cent Brewery” – Alec MacDonald – Elite Daily

Bacteria from Burning Tree mastodon survived 13,000 years – Laura Arenschield – Dispatch

Echo Bay woman caught harvesting bacteria at gardening event – Jeff Klassen – Soo Today

Weakened coral reefs are facing the threat of algae colonisation – Kemal Atlay – SBS Australia

Junk Food Is Bad For Plants, Too – How a steady diet of fertilizers has turned crops into couch potatoes – Anne Biklé and David R. Montgomery – Nautilus

From running shoes to carbon sinks: four surprising uses for algae – ABC Future Tense

Science, publishing, and career

“Everyone” Downloads Research Papers Illegally – Science magazine just published a great piece on the utility of Sci-Hub. Unfortunately, its defense of its own business model is flawed – Justin Peters – Slate

April 24, 2016

Posted on by

Effect of gluten-free diet, broad and accurate taxonomic resolution with multiple genes, ice-nucleating bacteria, indoor bacteria, fungi, and archaea.

Human oral microbiome

Changes in the Oral Moisture and the Amount of Microorganisms in Saliva and Tongue Coating after Oral Ingestion Resumption: A Pilot Study -Natsuki Kishimoto – The Open Dentistry Journal

Human gut microbiome

The influence of a short-term gluten-free diet on the human gut microbiome – Marc Jan Bonder – Genome Medicine

Gut microbiota of Type 1 diabetes patients with good glycaemic control and high physical fitness is similar to people without diabetes: an observational study – C. J. Stewart – Diabetic Medicine

The Influence of Prebiotic Arabinoxylan Oligosaccharides on Microbiota Derived Uremic Retention Solutes in Patients with Chronic Kidney Disease: A Randomized Controlled Trial – Ruben Poesen – PLOS ONE

Minireview: Human microbiome versus food-borne pathogens: friend or foe – Jonathan Josephs-Spaulding – Applied Microbiology and Biotechnology

Opinion: Strain-level dissection of the contribution of the gut microbiome to human metabolic disease – Chenhong Zhang – Genome Medicine

Review: Impact of the gut microbiota on inflammation, obesity, and metabolic disease – Claire L. Boulangé – Genome Medicine

Review: Translational aspects of the microbiome—to be exploited – Edit Mikó – Cell Biology and Toxicology

Animal models

Statement of Retraction. Replication of Obesity and Associated Signaling Pathways Through Transfer of Microbiota From Obese-Prone Rats – Frank A Duca – Diabetes

Gene expression of Lactobacillus plantarum and the commensal microbiota in the ileum of healthy and early SIV-infected rhesus macaques – Benjamin L. Golomb – Scientific Reports

Intestinal Microbiota and Microbial Metabolites Are Changed in a Pig Model Fed a High-Fat/Low-Fiber or a Low-Fat/High-Fiber Diet – Sonja N. Heinritz – PLOS ONE

Plant, root, and soil microbiome

(also filed under New Techniques below) New insights in host-associated microbial diversity with broad and accurate taxonomic resolution – Matthew T. Agler – bioRxiv

Detection of plant growth enhancing features in psychrotolerant yeasts from Patagonia (Argentina) – María Cecilia Mestre – Journal of Basic Microbiology

Discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community – John M Gladden – Biofuels

Soil biochar amendment shapes the composition of N2O-reducing microbial communities – Johannes Hartera – Science of the Total Environment

Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands of the Qinghai-Tibetan Plateau – Yong Zhang – Science of the Total Environment

Water and extremophile microbiome

Ice-nucleating bacteria control the order and dynamics of interfacial water – Ravindra Pandey – Science Advances

Unicellular cyanobacteria Synechocystis accommodate heterotrophic bacteria with varied enzymatic and metal resistance properties – Anas Abdulaziz – Journal of Basic Microbiology

Establishment of a multi-species biofilm model and metatranscriptomic analysis of biofilm and planktonic cell communities – Yuya Nakamura – Applied Microbiology and Biotechnology

Evidence of adaptation, niche separation and microevolution within the genus Polaromonas on Arctic and Antarctic glacial surfaces – Jan Gawor – Extremophiles

Built environment microbiology

Fungal and Bacterial Communities in Indoor Dust Follow Different Environmental Determinants – Fabian Weikl – PLOS ONE

Presence of Archaea in the Indoor Environment and Their Relationships with Housing Characteristics – Sepideh Pakpour – Microbial Ecology

Food microbiology

Enhancing the sweetness of yoghurt through metabolic remodeling of carbohydrate metabolism in Streptococcus thermophilus and Lactobacillus delbrueckii subsp. Bulgaricus – Kim I. Sørensen – Applied and Environmental Microbiology

Microbiota of an Italian Grana like cheese during manufacture and ripening unraveled by 16S rRNA-based approaches – Valentina Alessandria – Applied and Environmental Microbiology

Taxonomy, new techniques, bioinformatics

New insights in host-associated microbial diversity with broad and accurate taxonomic resolution – Matthew T. Agler – bioRxiv

Wedding higher taxonomic ranks with metabolic signatures coded in prokaryotic genomes – Gregorio Iraola – bioRxiv

Reviews: Eco-Evo-Devo: developmental symbiosis and developmental plasticity as evolutionary agents – Scott F. Gilbert – Nature Reviews Genetics

Microbes in the news

How the world’s chillest bacteria make ice. They may be responsible for creating clouds and rain – Alessandra Potenza – The Verge

How The Bacteria In Your Gut Could Be Used To Treat Mental Illness. New research finds that altering gut bacteria in mice changes the way their brains work – Carolyn Gregoire – Huffington Post

Five ‘fake’ water firms in Mombasa shut after tests confirm bacteria – Elkana Jacob – The Star Kenya

Investigators reduce sugar content of yogurt without reducing sweetness: using microbiological methods that predate the era of genetic technologies – Science Daily

How Toronto’s germs are different from those in other cities. New study reveals each community has its own unique blend of fungi and bacteria — a microbial signature – Robin Levinson King – The Star

Microbes and art

Living Art: Meet the Woman Making Sculptures With Bacteria from Her Skin, UK-based artist Mellissa Fisher – Stephanie Leke – Broadly The Vice