Category Archives: Human oral

June 24, 2015

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Chinese mushroom might help with weight loss (in mice), asthma and the microbiome (also in mice), metabolic networks in the gut, and benefits of resistant starch. Plus: Taylor Swift won’t be doing anymore reviewing for Nature.

Human oral microbiome

Alterations of Bacteroides sp., Neisseria sp., Actinomyces sp., and Streptococcus sp. populations in the oropharyngeal microbiome are associated with liver cirrhosis and pneumonia – Haifeng Lu – BMC Infectious Diseases

Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses – Jiazhen Chen – PLOS ONE

Human gut microbiome

Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology – Maria Carlota Dao – Gut

Animal models

Ganoderma lucidum reduces obesity in mice by modulating the composition of the gut microbiota – Chih-Jung Chang – Nature Communications

Evidence that asthma is a developmental origin disease influenced by maternal diet and bacterial metabolites – Alison N. Thorburn – Nature Communications

Characterization of the bacterial gut microbiota of piglets suffering from new neonatal porcine diarrhoea – Marie Louise Hermann-Bank – BMC Veterinary Research

Animal microbiome

Allometry of animal–microbe interactions and global census of animal-associated microbes – Thomas L. Kieft, Karen A. Simmons – Proceedings B

Introduction of Non-Native Pollinators Can Lead to Trans-Continental Movement of Bee-Associated Fungi – Shannon M. Hedtke – PLOS ONE

Effect of poly-β-hydroxybutyrate on growth, enzyme activity and intestinal microbial community of Chinese mitten crab, Eriocheir sinensis (Milne-Edwards) juveniles – Liying Sui – Aquaculture Research

Small stonefly predators affect microbenthic and meiobenthic communities in stream leaf packs – Nabil Majdi – Freshwater Biology

Plant, root and soil microbiome

Hologenome theory supported by co-occurrence networks of species-specific bacterial communities in siphonous algae (Caulerpa) – T. Aires – FEMS Microbial Ecology

Land Use History Shifts In Situ Fungal and Bacterial Successions following Wheat Straw Input into the Soil – Vincent Tardy – PLOS ONE

Water microbiome

Inefficient microbial production of refractory dissolved organic matter in the ocean – Helena Osterholz – Nature Communications

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation – Maryam Yazdani Foshtomi – PLOS ONE

Functional foods

Review: Preparation, health benefits and applications of resistant starch—a review – Bilal Ahmad Ashwar – Starch – Stärke

Metabolic networks and metabolomics

Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome – Steven N. Steinway – PLOS Computational Biology

A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fat – Rong Xu – BMC Genomics

Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism – Akram Mohammed – BMC Genomics

Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks – Hugo Roume – NPJ Biofilms and Microbiomes

Use of the Analysis of the Volatile Faecal Metabolome in Screening for Colorectal Cancer – Claire A Batty – PLOS ONE

Microbes in the news

IndieGoGo project: A Probiotic Life: Microbiome Documentary

New colon cancer culprit found in gut microbiome – EurekAlert

Mushroom used in Chinese medicine ‘slows weight gain’ – James Gallagher – BBC News

Announcing the uBiome Studies Portal “We’re aiming to launch one new study every week.” – uBiome

What is the role of the gut microbiome in developing Parkinson’s disease? – EurekAlert

Microbiology and art

Artists Reveal the Bacterial Beauty of the Human Microbiome – Shaunacy Ferro – Mental Floss

Science, publishing, and career

A day in the life of a malaria researcher – Lin Lee – BioMedCentral Blogs

Towards an unbiased view of science: Authors at Nature Communications now have the option to choose double-blind peer review – Nature Communications

Satire: Taylor Swift Announces She Will No Longer Review For Nature – The Allium

Bik’s Picks

A Middle Triassic stem-turtle and the evolution of the turtle body plan – Rainer R. Schoch & Hans-Dieter Sues – Nature

Scientists Finally Decide Which Bit of This Weird Animal is the Head – Ed Yong – National Geographic

America’s Next Top Chef is a Supercomputer From IBM – Liz Stinson – Wired
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June 21, 2015

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An upcoming workshop on bioinformatics and microbiome, lots of reviews about the intersection of gut microbiome and the immune system, and viruses in Arctic freshwater.

Events

NIMBioS Investigative Workshop: Computational Advances in Microbiome Research – July 27-28, 2015, University of Tennessee, Knoxville

Human oral microbiome

Salivary microbiota-immune profiling in cirrhosis: Could this be the noninvasive strategy that will revolutionize prognostication in hepatology? – Vishal C. Patel – Hepatology

Human gut microbiome

Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria – Weiwei Wang – Inflammatory Bowel Diseases

Review: Interactions between Innate Immunity, Microbiota, and Probiotics – GianMarco Giorgetti – Journal of Immunology Research

Review: Influence of the microbiome on response to vaccination – Amanda M. Jamieson – Human Vaccines & Immunotherapeutics

Review: How the Intricate Interaction among Toll-Like Receptors, Microbiota, and Intestinal Immunity Can Influence Gastrointestinal Pathology – Simona Frosali – Journal of Immunology Research

Review: The Interaction among Microbiota, Immunity, and Genetic and Dietary Factors Is the Condicio Sine Qua Non Celiac Disease Can Develop – D. Pagliari – Journal of Immunology Research

Review: Molecular methods for studying methanogens of the human gastrointestinal tract: current status and future directions – Prem Prashant Chaudhary – Applied Microbiology and Biotechnology

Animal models

Alterations of the Murine Gut Microbiome with Age and Allergic Airway Disease – Marius Vital – Journal of Immunology Research

DGGE: Alteration of the Microbiota and Virulence Gene Expression in E. coli O157:H7 in Pig Ligated Intestine with and without AE Lesions – Bianfang Liu – PLOS ONE

Animal microbiome

The coral immune response facilitates protection against microbes during tissue regeneration – Jeroen A. J. M. van de Water – Molecular Ecology

Plant microbiome

DGGE: Endophytic bacterial diversity in the phyllosphere of Amazon Paullinia cupana associated with asymptomatic and symptomatic anthracnose – Andréa Cristina Bogas – Springer Plus

Plant root, soil, and sediment microbiome

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study – A. Peyton Smith – Global Change Biology

Oil Biodegradation and Oil-degrading Microbial Populations in Marsh Sediments Impacted by Oil from the Deepwater Horizon Well Blowout – Ronald M Atlas – Environmental Science & Technology

Water microbiome

Biodiversity and distribution of polar freshwater DNA viruses – Daniel Aguirre de Cárcer – Science Advances

Baseline Assessment of Mesophotic Reefs of the Vitória-Trindade Seamount Chain Based on Water Quality, Microbial Diversity, Benthic Cover and Fish Biomass Data – Pedro M. Meirelles – PLOS ONE

Vertical Distribution of Bacterial Community Diversity and Water Quality during the Reservoir Thermal Stratification – Hai-Han Zhang – International Journal of Environmental Research and Public Health

Occurrence of Enterococcus species with virulence markers in an urban flow-influenced tropical recreational beach – Asmat Ahmad – Marine Pollution Bulletin

Microbes in the news

International Team Profiles DNA Viruses in Arctic Freshwater Lakes – Genome Web

Why is my hangover so bad? It’s not just the booze giving you a hangover – it’s the microbes in your stomach – Tim Spector

Israel Bets On Recycled Water To Meet Its Growing Thirst – Emily Harris – NPR

Science, publishing and career

Distraction Coefficients of Females in Biomedical Research Laboratories – Chi R. Ality – Significance

Bik’s Picks

Stanford researcher declares that the sixth mass extinction is here – Rob Jordan – Stanford University

A Periodic Diet that Mimics Fasting Promotes Multi-System Regeneration, Enhanced Cognitive Performance, and Healthspan – Sebastian Brandhorst – Cell Metabolism

Eating up to 100 g of chocolate daily linked to lowered heart disease and stroke risk – BMJ’s Heart
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June 20, 2015

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Catching up after spending all day in the lab on Friday, and all day working on figures and text today…. Here’s your weekend digest, with the microbiome of sport schools, phasing of Illumina sequencing, and happy endings for preterm infants.

Pregnancy and birth microbiome

Preterm infant gut colonization in the Neonatal ICU and Complete Restoration two years later – Laura Moles – Clinical Microbiology and Infection

Clostridium butyricum strains and dysbiosis linked to necrotizing enterocolitis in preterm neonates – Nadim Cassir – Clinical Infectious Diseases

Human respiratory microbiome

The microbiome of the human lower airways: a next generation sequencing perspective – Velma T. E. Aho – World Allergy Organization Journal

Human skin microbiome

Poster: Noma disease: 10 years of research in the quest of a microbial etiology – P François – Antimicrobial Resistance and Infection Control

Human oral microbiome

Oral Mucositis in Pediatric Acute Lymphoblastic Leukemia Patients: Evaluation of Microbiological and Hematological Factors – Regina Maria Holanda de Mendonça – Pediatric Hematology-Oncology

Human gut microbiome

Composition and temporal stability of the gut microbiota in older persons – Ian B Jeffery – The ISME Journal

The Host Genotype and Environment Affect Strain Types of Bifidobacterium longum subsp. longum Inhabiting the Intestinal Tracts of Twins – Min Zhang – Applied and Environmental Microbiology

The Influence of the Gut Microbiome on Obesity, Metabolic Syndrome and Gastrointestinal Disease – Parth J Pareck – Clinical and Translational Gastroenterology

Editorial: About the gut microbiome as a pharmacological target in atherosclerosis – Julia.J. Witjes – European Journal of Pharmacology

Editorial: Diabetes, More on Merde, the Microbiome, and the Dung Beetle – Richard I. Shader – Clinical Therapeutics

Review: Effect of Dietary Resistant Starch on Prevention and Treatment of Obesity-related Diseases and Its Possible Mechanisms – Lei Zhang – Biomedical and Environmental Sciences

Animal models

In pigs: Influence of genotype and feeding strategy on pig performance, plasma concentrations of micro nutrients, immune responses and fecal microbiota composition of growing-finishing pigs in a forage-based system – A.G. Kongsted – Livestock Science

In rats: Prenatal Stress-Induced Alterations in Major Physiological Systems Correlate with Gut Microbiota Composition in Adulthood – Anna V. Golubeva – Psychoneuroendocrinology

In mice: The genetic architecture of NAFLD among inbred strains of mice – Simon T Hui – eLIFE

Animal microbiome

Cows: Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency – Kelsea A. Jewell – Applied and Environmental Microbiology

Thesis: The earthworm microbiome – Daniel Antony Pass – Cardiff University

Thesis: Gut microbiota of migratory passerines at stopover – William Lewis – University of Southern Mississippi

Plant microbiome

PERN: an EU–Russia initiative for rhizosphere microbial resources – Stéphane Declerck – Trends in Biotechnology

Review: Biological control in the microbiome era: challenges and opportunities – Haissam Jijakli – Biological Control

Plant root and soil microbiome

Impact of plant domestication on rhizosphere microbiome assembly and functions
Juan E. Pérez-Jaramillo – Plant Molecular Biology

16S rRNA-based bacterial community structure is a sensitive indicator of soil respiration activity – Rongxiao Che – Journal of Soils and Sediments

Built environment microbiome

Athletic equipment microbiota are shaped by interactions with human skin – Mariah Wood – Microbiome

Food microbiology

Bacteriophages Isolated from Chicken Meat and the Horizontal Transfer of Antimicrobial Resistance Genes – Amira Shousha – Applied and Environmental Microbiology

Microbiological diversity associated with the spontaneous wet method of coffee fermentation – Suzana Reis Evangelista – International Journal of Food Microbiology

Chemical and microbiological characteristics of traditional homemade fresh goat cheeses from Northern Morocco – Ouiam El Galiou – Small Ruminant Research

Metagenomics and bioinformatics

Microbial bioinformatics for food safety and production – Wynand Alkema – Briefings in Bioinformatics

Niche distribution and influence of environmental parameters in marine microbial communities: a systematic review – Felipe H. Coutinho – Peer J

Ultra-large alignments using phylogeny-aware profiles – Nam-phuong D Nguyen – Genome Biology

Techiques

Phasing amplicon sequencing on Illumina Miseq for robust environmental microbial community analysis – Liyou Wu – BMC Microbiology

Microbes in the news

Medicine’s next frontier: The microbiome – Meg Tirrell – CNBC

Microbes could be key for better yields, stronger plants – Michigan State University – AG Professional

Berkeley balcony collapse: A failure at the intersection of building science and microbiology – Brent Stephens – Microbe.net

Science, publishing, and career

Gender Differences in Physicians’ Financial Ties to Industry: A Study of National Disclosure Data – Susannah L. Rose – PLOS ONE

“If you think it’s rude to ask to look at your co-authors’ data, you’re not doing science” – C. K. Gunsalus and Drummond Rennie – Retraction Watch

Bik’s Picks

An Ant With the Right Coat for 158-Degree Weather – Sindya N. Bhanoo – New York Times

8 million mummified animals, mostly dogs, in catacombs at Egypt site – Greg Botelho – CNN

Blind Americans can now ‘see’ with a device that uses their tongues – Michelle Cortez – Mashable

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June 17, 2015

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After a long day in the hood having fun with stool samples (Ha! I hope you are not reading this during breakfast), finally time for the digest.

Microbiome of pregnancy and birth

Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case – Jacque C. Young – Proteomics

Mouse model: Alterations in the Vaginal Microbiome by Maternal Stress Are Associated With Metabolic Reprogramming of the Offspring Gut and Brain – Eldin Jašarević- Endocrinology

Human oral microbiome

Subgingival microbiome in patients with healthy and ailing dental implants – Hui Zheng – Scientific Reports

Human gut microbiome

Editorial: The Interactions between Innate Immunity and Microbiota in Gastrointestinal Diseases – Danilo Pagliari – Journal of Immunology Research

Animal microbiome

Microbial diversity associated with copepods in the North Atlantic subtropical gyre – Katyanne M. Shoemaker – FEMS Microbiology Ecology

Plant microbiome

Bacterial populations on the surfaces of organic and conventionally grown almond drupes – J.A. McGarvey – Journal of Applied Microbiology

Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific – Tao Zhang – PLOS ONE

Plant root and soil microbiome

High resolution depth distribution of Bacteria, Archaea, methanotrophs, and methanogens in the bulk and rhizosphere soils of a flooded rice paddy – Hyo Jung Lee – Frontiers in Microbiology

Profiling microbial community structures across six large oilfields in China and the potential role of dominant microorganisms in bioremediation – Weimin Sun – Applied Microbiology and Biotechnology

Influence of Pre-Emergence Herbicides on the Soil Microflora during the
Crop growth of Blackgram, Vigna mungo.L – N.Trimurtulu – Int.J.Curr.Microbiol.App.Sci

Metagenomics and Bioinformatics

GenomePeek—an online tool for prokaryotic genome and metagenome analysis – Katelyn McNair – PeerJ

Deconvolving molecular signatures of interactions between microbial colonies – Y.-C. Harn – Bioinformatics

Reconstructing 16S rRNA genes in metagenomic data – Cheng Yuan – Bioinformatics

Microbes in the news

Below Our Feet, a World of Hidden Life – Elizabeth Svoboda – Quanta Magazine

Maternal stress alters offspring gut, brain through vaginal microbiome – Science Daily

Big Shoulders STEM Scholars – Dr Jack Gilbert explains the latest microbiome research to students; A short artwork project with artist Katharine Gilbert was completed at the end. – YouTube

BacteriaHysteria

This reminded me of the door scene from Office Space: Germ-Zapping Doorknob Could Get a Handle on Bathroom Bacteria – TakePart

Bik’s Picks

An Estimate of the Total DNA in the Biosphere – Hanna K. E. Landenmark – PLOS Biology

New NASA data show how the world is running out of water – Todd C. Frankel – The Washington Post

Tiny Octopus Is So Cute Scientists Might Name It ‘Adorabilis’ – Carl Enkelking – Discover Magazine
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June 16, 2015

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Human oral microbiome

The cultivable microbiota of primary and secondary infected root canals, their susceptibility to antibiotics and association with the signs and symptoms of infection – M. E. Łysakowska – International Endodontic Journal

DGGE: Profiling of Oral and Nasal Microbiome in Children With Cleft Palate – Min Zhang – The Cleft Palate–Craniofacial Journal

Human gut microbiome

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates – Doris Vandeputte – Gut

Bacterial Composition of the Human Upper Gastrointestinal Tract Microbiome Is Dynamic and Associated with Genomic Instability in a Barrett’s Esophagus Cohort – Alevtina Gall – PLOS ONE

Alterations in Intestinal Microbiota Correlate with Susceptibility to Type 1 Diabetes – Aimon K. Alkanani – Diabetes

Specific gut microbiota features and metabolic markers in postmenopausal women with obesity – LK Brahe – Nutrition & Diabetes

Inter- and intra-individual variations in seasonal and daily stabilities of the human gut microbiota in Japanese – Takayoshi Hisada – Archives of Microbiology

Editorial: Gut bacteria feed a healthy brain – Denise Waldron – Nature Reviews Microbiology

Review: The gut microbiota of nonalcoholic fatty liver disease: current methods and their interpretation – Niels van Best – Hepatology International

Review: Can we change our microbiome to prevent colorectal cancer development? – Roberta M. Manzat-Saplacan – Acta Oncologica

Human genital microbiome

Penile Microbiota and Female Partner Bacterial Vaginosis in Rakai, Uganda – Cindy M. Liu – mBio

Models of microbiome

In pigs: Neonatal environment exerts a sustained influence on the development of the intestinal microbiota and metabolic phenotype – Claire A Merrifield – ISME Journal

In goats: Postnatal bacterial succession and functional establishment of hindgut in supplemental feeding and grazing goats – J. Z. Jiao – Journal of Animal Science

In termites: Multiple analyses of microbial communities applied to the gut of the wood-feeding termite Reticulitermes flavipes fed on artificial diets – Cédric Tarayre – Symbiosis

Animal microbiome

Sponges: Pyrosequencing revealed shifts of prokaryotic communities between healthy and disease-like tissues of the Red Sea sponge Crella cyathophora – Zhao-Ming Gao – PeerJ

Sponges: Microbial diversity and putative diazotrophy in high and low microbial abundance Mediterranean sponges – Marta Ribes – Applied and Environmental Microbiology

Plant root and soil microbiome

Tree genotype mediates covariance among communities from microbes to lichens and arthropods – Louis J. Lamit – Journal of Ecology

Assessment of microbial communities in mung bean (Vigna radiata) rhizosphere upon exposure to phytotoxic levels of Copper – Murali Sharaff – Journal of Basic Microbiology

Analyzing the antagonistic potential of the lichen microbiome against pathogens by bridging metagenomic with culture studies – Tomislav Cernava – Frontiers in Microbiology

Response of rhizosphere microbial community structure and diversity to heavy metal co-pollution in arable soil – Linjing Deng – Applied Microbiology and Biotechnology

Soil Microbial Functions After Forest Fires Affected by the Compost Quality – René Guénon – Land Degradation & Development

Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning – Xian Liu – Microbial Ecology

Metagenome Sequencing Reveals Rhodococcus Dominance in Farpuk Cave, Mizoram, India, an Eastern Himalayan Biodiversity Hot Spot Region – Surajit De Mandal – Genome Announcements

The stability of textile azo dyes in soil and their impact on microbial phospholipid fatty acid profiles – Muhammad Imran – Ecotoxicology and Environmental Safety

Endophyte community composition is associated with dieback occurrence in an invasive tree – Tracey V. Steinrucken – Plant and Soil

Multi-Analytical Approach Reveals Potential Microbial Indicators in Soil for Sugarcane Model Systems – Acacio Aparecido Navarrete – PLOS ONE

Resilience of soil microbial and nematode communities after biofumigant treatment with defatted seed meals – S. Mocali – Industrial Crops and Products

Effect of cassava mill effluent on biological activity of soil microbial community – Etinosa O. Igbinosa – Environmental Monitoring and Assessment

Editorial: An interkingdom partnership – Naomi Attar – Nature Reviews Microbiology

Review: Synergisms between microbial pathogens in plant disease complexes: a growing trend – Jay Ram Lamichhane – Frontiers in Plant Science

Review: Plant Virus Metagenomics: Advances in Virus Discovery – Marilyn J. Roossinck – Phytopathology

Water microbiome

Microbial ecology in a future climate: effects of temperature and moisture on microbial communities of two boreal fens – Krista Peltoniemi – FEMS Microbiology Ecology

A Multi Size-Level Assessment of Benthic Marine Communities in a Coastal Environment: Are They Different Sides of the Same Coin? – Claudia Vannini – PLOS ONE

Manganese-Cycling Microbial Communities Inside Deep-Sea Manganese Nodules – Marco Blöthe – Environmental Science & Technology

Editorial: Deep sequencing of the global oceans – Cláudio Nunes-Alves – Nature Reviews Microbiology

Extremophile microbiome

Microbial diversity of hypersaline environments: a metagenomic approach – Antonio Ventosa – Current Opinion in Microbiology

Application of a Bayesian nonparametric model to derive toxicity estimates based on the response of Antarctic microbial communities to fuel-contaminated soil – Julyan Arbel – Ecology and Evolution

Bioreactor microbiome

Evaluation of surfactants on waste activated sludge fermentation by pyrosequencing analysis – Aijuan Zhou – Bioresource Technology

Impact of the contemporary environment on denitrifying bacterial communities – Sarah K. Hathaway – Ecological Engineering

Food microbiology

Review: Wine microbiome, a dynamic world of microbial interactions – Youzhong Liu

Metagenomics and bioinformatics

Unusual biology across a group comprising more than 15% of domain Bacteria – Christopher T. Brown – Nature

Complete Genome Sequence of the Bacterium Aalborg_AAW-1, Representing a Novel Family within the Candidate Phylum SR1 – Morten Simonsen Dueholm – Genome Announcements

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs – Felipe A. Simão – Bioinformatics

Educating Future Nursing Scientists: Recommendations for Integrating Omics Content in PhD Programs – Yvette P. Conley – Nursing Outlook

Minireview: Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: Towards a systems-level understanding of human microbiomes – Bikel Shirley – Computational and Structural Biotechnology Journal

Metabolomics and Proteomics

In dogs: Consumption of Cooked Navy Bean Powders Modulate the Canine Fecal and Urine Metabolome – M. Forster – Current Metabolomics

Needles in the Blue Sea: Sub-Species Specificity in Targeted Protein Biomarker Analyses Within the Vast Oceanic Microbial Metaproteome – Mak A. Saito – Proteomics

New aminopeptidase from “microbial dark matter” archaeon – Karolina Michalska – The FASEB Journal

Review: Recent Advances in Metabolomics – E. Smith – Current Metabolomics

Microbial Ecology

Transplantability of a circadian clock to a noncircadian organism – Anna H. Chen – Science Advances

Review: Black Queen evolution: the role of leakiness in structuring microbial communities – J. Jeffrey Morris – Trends in Genetics

Techniques

Preferential Amplification of Pathogenic Sequences – Fang Ge – Scientific Reports

Phasing of single DNA molecules by massively parallel barcoding – Erik Borgström – Nature Communications

Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of
SAR11 bacterioplankton – Amy Apprill – Aquatic Microbial Ecology

Microbes in the news

Newfound groups of bacteria are mixing up the tree of life – Robert Sanders – UC Berkeley

Report: Santa Cruz’s river bacteria comes from birds, not people – Samantha Clark – San Jose Mercury News

Shark Tank Product Improves Oral Health, Measuring Levels Of Bacteria That Cause Bad Breath – Samantha Olson – Medical Daily

Manatee County, not the animal: Bacteria Could Clean Manatee Water Supply – Associated Press

Bacteria Could Help Clean Groundwater Contaminated by Uranium Ore Processing, Rutgers Study Finds – Rutgers Today

BacteriaHysteria

How much bacteria is on money in your pocket? – Click2Houston

WHO: 200 disease-causing bacteria may be found in the kitchen – ABC/CBN news

Science, publishing, and career

Science forum: RIPOSTE: a framework for improving the design and analysis of laboratory-based research – Nicholas GD Masca – eLIFE

Dancers in the Dark: Scientific Careers According to a Gender-Blind Model of Promotion –
Ana M. González Ramos – Interdisciplinary Science Reviews

Incidence of Data Duplications in a Randomly Selected Pool of Life Science Publications – Morten P. Oksvold – Science and Engineering Ethics

Five things I learned when my research went viral – Heidi Appel – The Conversation

Bik’s Picks

Foie Gras: The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver – Lizhi Lu – Genome Biology

An estimate of the number of tropical tree species – JW Ferry Slik – PNAS

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June 9, 2015

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Job openings for microbiome leaders in Pittsburgh, functional foods and microbial growth, and lots of reviews and editorials.

Jobs

The new Center for Microbiome and Medicine at the University of Pittsburgh is hiring leader(s) in microbiome research

Microbiome of pregnancy and birth

Review: Early microbial contact, breast milk microbiome and child health – S. Rautava – Journal of Developmental Origins of Health and Disease

Human oral microbiome

Screening of Probiotic Candidates in Human Oral Bacteria for the Prevention of Dental Disease – Tomohiko Terai – PLOS ONE

Review: Do oral bacteria alter the regenerative potential of stem cells? A concise review – Kyriaki Chatzivasileiou – Journal of Cellular and Molecular Medicine

Human gut microbiome

Editorial for David et al.’s cholera recovery paper: A gut instinct for recovery – Naomi Attar – Nature Reviews Microbiology

Letter to the Editor: Altered microbiota in microscopic colitis – Hans Fischer – Gut

Letter to the Editor: Colonisation with multidrug-resistant bacteria is associated with increased mortality in patients with cirrhosis – Oliver Waidmann – Gut

Animal microbiome

Review: The animal gut as a melting pot for horizontal gene transfer – N. Shterzer, I. Mizrahi – Canadian Journal of Microbiology

Plant root and soil microbiome

Assessment of rhizospheric culturable bacteria of Phragmites australis and Juncus effusus from polluted sites – Sofia I.A. Pereira – Journal of Basic Microbiology

Review: Dispersing misconceptions and identifying opportunities for the use of ‘omics’ in soil microbial ecology – Nature Reviews Microbiology

Built environment microbiome

The effects of different hygiene procedures in reducing bacterial contamination in a model domestic kitchen – Elin Røssvoll – Journal of Applied Microbiology

Functional foods

Pomegranate Ellagitannins Stimulate Growth of Gut Bacteria In Vitro: Implications for Prebiotic and Metabolic Effects – Zhaoping Li – Anaerobe

Prebiotics Modulate the Effects of Antibiotics on Gut Microbial Diversity and Functioning in Vitro – Laura P. Johnson – Nutrients

Microbes in the news

From World Aquaculture 2015: “The gut microbiome of farmed trout is far more complex than previous research has documented” – Alltech highlights latest research in farmed trout – Undercurrent News

How the ‘Microbiome’ Affects Your Baby’s Birth and Health – Penny Simkin – Seattle PI

MicroBiome Therapeutics Presents Clinical Data On Diabetes Drug NM505 At ADA’s 75th Scientific Sessions And Reports Issuance Of NM505 Patent – PR Newswire

Here’s What Happens When You Culture The Bacteria on an Eight Year Old’s Hand – Marissa Fessenden – Smithsonian

MERS Is Not SARS, but Control Was Poor: Seoul ID Docs – Outbreak claims seventh fatality as specialists acknowledge poor infection control – MedPage Today

Bik’s Picks

Massage-like stroking boosts the immune system in mice – Benjamin Major – Scientific Reports

Just add water: Stanford engineers develop a computer that operates on water droplets – Stanford News

A crummy dinosaur fossil turns out to hold 75 million-year-old blood and proteins – Rachel Feltman – The Washington Post

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June 8, 2015

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General microbiome

Minireview: The brain’s Geppetto—microbes as puppeteers of neural function and behaviour? – Roman M. Stilling – Journal of NeuroVirology

Thesis: Novel computational approaches to investigate microbial diversity – Qingpeng Zhang – Michigan State University

Microbiome of pregnancy and birth

Distinctive Intestinal Lactobacillus Communities in Six-Month-Old Infants From Rural Malawi and South-Western Finland – Aakko, Juhani – Journal of Pediatric Gastroenterology & Nutrition

Antenatal Microbiome: Potential Contributor to Fetal Programming and Establishment of the Microbiome in Offspring – Michelle L. Wright, Angela R. Starkweather – Nursing Research

Review: Should Abnormal Vaginal Flora in 2 nd Trimester of Pregnancy be Treated to Prevent Preterm Labor – Gunjan Kumari, Anjali Tempe – Journal of Medical Sciences

Human oral microbiome

The oral mucosal and salivary microbial community of Behcet’s syndrome and recurrent aphthous stomatitis – Noha Seoudi – Journal of Oral Microbiology

Human gut microbiome

Review: Unraveling the environmental and genetic interactions in atherosclerosis: Central role of the gut microbiota – Elin Org – Atherosclerosis

Review: The Effects of Diet and the Microbiome on Reproduction and Longevity: A Comparative Review Across 5 Continents – Stephanie N. Chilton – Nutrition and Food Sciences

Animal models of microbiome research

Lack of Vitamin D Receptor Causes Dysbiosis and Changes the Functions of the Murine Intestinal Microbiome – Dapeng Jin – Clinical Therapeutics

Animal microbiome

Acromyrmex leaf-cutting ants have simple gut microbiota with nitrogen-fixing potential – Panagiotis Sapountzis – Applied and Environmental Microbiology

Anemone: Response of bacterial colonization in Nematostella vectensis to development, environment and biogeography – Benedikt Mortzfeld – Environmental Microbiology

Plant root and soil microbiome

Responses of bacterial communities in seagrass sediments to polycyclic aromatic hydrocarbon-induced stress – Juan Ling – Ecotoxicology

Analyses of microbial biomass and community diversity in kiwifruit orchard soils of different planting ages – Qingxia Fu – Acta Ecologica Sinica

The effects of the presence of Bt-transgenic oilseed rape in wild mustard populations on the rhizosphere nematode and microbial communities – Yongbo Liu – Science of The Total Environment

Long-term conservation tillage influences the soil microbial community and its contribution to soil CO2 emissions in a Mollisol in Northeast China – Shuxia Jia – Journal of Soils and Sediments

Microbial communities inhabiting oil-contaminated soils from two major oilfields in Northern China: Implications for active petroleum-degrading capacity – Weimin Sun – Journal of Microbiology

Differential degradation of polycyclic aromatic hydrocarbon mixtures by indigenous microbial assemblages in soil – Przemyslaw Sawulski – Letters in Applied Microbiology

A novel salt-tolerant chitobiosidase discovered by genetic screening of a metagenomic library derived from chitin-amended agricultural soil – Mariana Silvia Cretoiu – Applied Microbiology and Biotechnology

Book chapter: Irrigation with Treated Wastewater: Potential Impacts on Microbial Function and Diversity in Agricultural Soils – Ana Rita Lopes – The Handbook of Environmental Chemistry 2015

Water microbiome

Response of bacteria and meiofauna to iron oxide colloids in sediments of freshwater microcosms – Sebastian Höss – Environmental Toxicology and Chemistry

Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site – Federico Baltar – FEMS Microbiology Ecology

Book Chapter: Marine Litter as Habitat and Dispersal Vector – Tim Kiessling – Marine Anthropogenic Litter

Thesis: Metagenomic profiling of microbial metal interaction in Red Sea deep-anoxic brine pools – Hanna, Mina Magdy Abdelsayed – American University in Cairo

Built environment microbiome

Microbial community composition of a household sand filter used for arsenic, iron, and manganese removal from groundwater in Vietnam – Katja Sonja Nitzsche – Chemosphere

The role of bacterial communities and carbon dioxide on the corrosion of steel – K.M. Usher – Corrosion Science

Extremophile microbiome

Review: Metagenomics of extreme environments – DA Cowan – Current Opinion in Microbiology

Food microbiology

Review: The impact of climate change on existing and emerging microbial threats across the food chain: An island of Ireland perspective – Linda D. Stewart – Trends in Food Science & Technology

Review: Microbial decontamination of food by electron beam irradiation – Hsiang-Mei Lung – Trends in Food Science & Technology

Bioreactor microbiome

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unraveled with genome-resolved metagenomics – Rose S. Kantor – Environmental Microbiology

Bioinformatics and metagenomics

CCLasso: Correlation Inference for Compositional Data through Lasso – Huaying Fang – Bioinformatics

GAML: genome assembly by maximum likelihood: combination of diverse sequencing datasets into a single assembly – Vladimír Boža – Algorithms for Molecular Biology

Effects of library size variance, sparsity, and compositionality on the analysis of microbiome data – Sophie J Weiss – PeerJ

Review: Identification of Viruses and Viroids by Next-Generation Sequencing and Homology-Dependent and Homology-Independent Algorithms – Qingfa Wu – Annual Reviews Phytopathology

Metabolomics

Mapping microbial response metabolomes for induced natural product discovery – Dagmara K. Derewacz – ACS Chemical Biology
http://pubs.acs.org/doi/abs/10.1021/acschembio.5b00001

Techniques

Analysis of microsamples of human faeces: a non-invasive approach to study the bioavailability of fat-soluble bioactive compounds – E. Hernandez-Alvarez – European Journal of Nutrition

Microbes in the news

Say hello to your little friends: Making sense of gut bacteria – Wency Leung – Globe and Mail

Surfers help science in fight against antibiotic resistant bacteria with their poop – Luigi Lugmayer – i4u

Effects of zinc oxide on intestinal microbiota – All About Feed

Video: Waxworm Bacteria Could Recycle Plastic Trash – NBC News

Is That Water Hot Enough to Kill Germs? – C. Claiborne Ray – New York Times

Gut bacteria play a vital role to your health – Sharon Ní Chonchuir – Irish Examiner

New microscope technique could speed identification of deadly bacteria – EurekAlert

Science, publishing, and career

Better advice for ‘Bothered’ – Science Careers Staff – Science Magazine

Retractions and High Profile Journals – Peter Edmonds

Bik’s Picks

Black Hole Hunters – Dennis Overbye – New York Times

Everything You Need to Know About Bill Nye’s Crazy Experimental Spaceship – Jack Linshi – Time

Under the Sea: Google Views for World Oceans Day – Patrick J. Kiger – Discovery

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June 6, 2015

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A new paper on the microbiome of the human nose, several gut microbiome reviews,  microbiomes of soils and extreme environments, microbiome models and a cool poster about defining OTU. Happy Saturday!

Human oral microbiome

Antimicrobial Effect of a Single Dose of Amoxicillin on the Oral Microbiota – Cecilia Larsson Wexell – Clinical Implant Dentistry and Related Research

Human respiratory microbiome

Staphylococcus aureus and the ecology of the nasal microbiome – Cindy M. Liu – Science Advances

Human gut microbiome

Review: Interactions between Diet, Bile Acid Metabolism, Gut Microbiota, and Inflammatory Bowel Diseases – Devkota S – Digestive Diseases

Review: Gut Microbiota, Cirrhosis, and Alcohol Regulate Bile Acid Metabolism in the Gut – Ridlon J.M – Digestive Diseases

Review: Relationship between Obesity, Gut Microbiome and Hepatocellular Carcinoma Development – Hara E. – Digestive Diseases

Animal models of microbiome research

Absence of the intestinal microbiota exacerbates hepatobiliary disease in a murine model of primary sclerosing cholangitis – James H. Tabibian – Hepatology

Effects of dietary fat profile on gut permeability and microbiota and their relationships with metabolic changes in mice – Yan Y. Lam – Obesity

Animal microbiome

Gut-Associated Bacteria of Dendroctonus valens and their Involvement in Verbenone Production – Letian Xu – Microbial Ecology

Feeding of β-1,3/1,6-glucan increases the diversity of the intestinal microflora of carp (Cyprinus carpio) – V. Jung-Schroers – Aquaculture Nutrition

Changes in coral reef communities across a natural gradient in seawater pH – Hannah C. Barkley – Science Advances

Plant root, soil and sediment microbiome

Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential – Alessandra Salvioli – ISME Journal

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes – Margarita Lopez-Fernandez – Microbial Ecology

Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity – Eric Capo – Microbial Ecology

Water microbiome

Phytoplankton community structure in relation to vertical stratification along a north-south gradient in the Northeast Atlantic Ocean – Kristina D. A. Mojica – Limnology and Oceanography

Extremophile microbiome

Supratidal Extremophiles—Cyanobacterial Diversity in the Rock Pools of the Croatian Adria – Maria Brandes – Microbial Ecology

Pyrosequencing-Based Assessment of the Microbial Community Structure of Pastoruri Glacier Area (Huascarán National Park, Perú), a Natural Extreme Acidic Environment – Elena González-Toril – Microbial Ecology

Metagenomics and bioinformatics

Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities – Markus Majaneva

Microbiome models, on computers and in lab dishes, see progress – Jop de Vrieze – Nature Medicine

Don’t miss this cool poster: OTU robustness, reproducibility and ecological consistency in the demarcation of operational taxonomic units – Thomas SB Schmidt

Microbes in the news

Nasal Microbiome Study Examines Influence of Host Genetics, Types of Bacterial Communities – Genome Web

The fastest-growing biome on Earth is in our homes. Forget your kids and pets. Your house’s biodiversity hotspots shelter tons of microorganisms – Mary Jo DiLonardo

Socialising Baboons and Gut Microbes – deSciphered: summarising research with simple graphics

Exploring the Link Between Gut Microbes and Diabetes – Betul Hatipoglu

Kaiser Permanente Fresno uses ‘zapper’ to get rid of deadly bacteria – ABC30

This Man Believes Mushrooms Can Solve Virtually All of Humanity’s Problems: next probiotic? – Munchies

Bik’s Picks

Eating placenta ‘does not benefit health’: There is no scientific evidence that eating the placenta after childbirth can protect women against depression and boost energy, US research suggests –  – BBC News

Ancient Shark Fossil Found in Texas – Deborah Grace – Pioneer News

Video: Robots Falling Down at DARPA Robotics Challenge – IEEE Spectrum – Youtube

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June 5, 2015

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A new test that reveals past viral infections using one drop of blood, subgingival microbiota in HIV-infected adults, and influencing horse behavior through diet.

Human oral microbiome

The oral mucosal and salivary microbial community of Behçet’s syndrome and recurrent aphthous stomatitis – Seoudi N – J Oral Microbiology

Subgingival bacterial community profiles in HIV-infected Brazilian adults with chronic periodontitis – D. C. Ferreira – Journal of Periodontal Research

Human bladder microbiome

Decreased microbiota diversity associated with urinary tract infection in a trial of bacterial interference – Deborah Horwitz – Journal of Infection

Human gut microbiome

Use of T-RFLP and seven restriction enzymes to compare the faecal microbiota of obese and lean Japanese healthy men – T. Kobayashi – Beneficial Microbes

The Gut Microbiome and Childhood Obesity: Connecting the Dots – An interview with Mueller Noel Theodore – Childhood Obesity

Review: Metagenomics of the Human Intestinal tract: From who is there to what is done there – Antonietta Cultrone – Current Opinion in Food Science

Editorial: On the Gut Microbiome-Brain Axis and Altruism – Theoharis C. Theoharides – Clinical Therapeutics

Review: Potential Etiologic Factors of Microbiome Disruption in Autism – Timothy Buie – Clinical Therapeutics

Conference abstract: Dietary supplementation with a type 3 resistant starch induces butyrate producing bacteria within the gut microbiota of human volunteers – J. Kelly – Appetite

Review: Immunogenetic control of the intestinal microbiota – Eric Marietta – Immunology

Book chapter: Fecal Microbiota Transplantation for Clostridium Difficile Infection: A Systematic Review of the Evidence – Dimitri Drekonja – Department of Veterans Affairs

Review: Gut bacteria and cancer – Susan E. Erdman – Biochimica et Biophysica Acta (BBA) – Reviews on Cancer

Review: The Gut Microbiota and Type 1 Diabetes – Elke Gülden – Clinical Immunology

Animal models of microbiome research

Transmissible microbial and metabolomic remodeling by soluble dietary fiber improves metabolic homeostasis – Baokun He – Scientific Reports

Antibiotics promote inflammation through the translocation of native commensal colonic bacteria – Kathryn A Knoop – Gut

Pyrosequencing reveals shifts in the bacterial epimural community relative to dietary concentrate amount in goats – S.U. Wetzels – Journal of Dairy Science

Programming rumen bacterial communities in newborn Merino lambs – I. De Barbieri – Small Ruminant Research

Changes of the hindgut microbiota due to high-starch diet can be associated with behavioral stress response in horses – Alexandra Destrez – Physiology & Behavior

Animal microbiome

Bats: Phyllostomid bat microbiome composition is associated to host phylogeny and feeding strategies – Mario Carrillo-Araujo – Frontiers in Microbiology

Squirrels: An Invasive Mammal (the Gray Squirrel, Sciurus carolinensis) Commonly Hosts Diverse and Atypical Genotypes of the Zoonotic Pathogen Borrelia burgdorferi Sensu Lato
Caroline Millins – Applied and Environmental Microbiology

Fish: High diversity of skin-associated bacterial communities of marine fishes is promoted by their high variability among body parts, individuals and species – Marlène Chiarello

Snakes: Phylogenetic Analysis of Bacterial Communities in Different Regions of the Gastrointestinal Tract of Agkistrodon piscivorus, the Cottonmouth Snake – Timothy J. Colston – PLOS ONE

Insects: Leaf-Cutter Ant Fungus Gardens Are Biphasic Mixed Microbial Bioreactors That Convert Plant Biomass to Polyols with Biotechnological Applications – Alexandre F. Somera – Applied and Environmental Microbiology

Nematodes: Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts – Kristen E. Murfin – mBio

Coral: Microbial invasion of the Caribbean by an Indo-Pacific coral zooxanthella – D. Tye Pettay – PNAS

Plant root and soil microbiome

Linking jasmonic acid signalling, root exudates and rhizosphere microbiomes – Lilia C Carvalhais – Molecular Plant-Microbe Interactions

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils – David A. Lipson – Environmental Microbiology Reports

Two decades of warming increases diversity of a potentially lignolytic bacterial community  – Grace Pold – Frontiers in Microbiology

Water microbiome

Patterns and Determinants of Halophilic Archaea (Class Halobacteria) Diversity in Tunisian Endorheic Salt Lakes and Sebkhet Systems – Afef Najjari – Applied and Environmental Microbiology

Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre – Kristina M. Fontanez – Frontiers in Microbiology

Metagenomic resolution of microbial functions in deep-sea hydrothermal plumes across the Eastern Lau Spreading Center – Karthik Anantharaman – The ISME Journal

Built environment microbiome

Inflammatory potential in relation to the microbial content of settled dust samples collected from moisture-damaged and reference schools: results of HITEA study – K. Huttunen

Pyrosequencing analysis of bacterial diversity in dental unit waterlines – Damien Costa – Water Research

Viruses and phages

Comprehensive serological profiling of human populations using a synthetic human virome – George J. Xu – Science

Metagenomics and 16S rRNA sequencing

Viewpoint: Improving the quality of genome, protein sequence, and taxonomy databases: a prerequisite for microbiome meta-omics 2.0 – Olivier Pible and Jean Armengaud – Proteomics

Opinion: Confusion about the species richness of human gut microbiota – E. Avershina, K. Rudi – Beneficial Microbes

Metabolomics

Microbial secondary metabolites in homes in association with moisture damage and asthma – P. V. Kirjavainen – Indoor Air

In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum “Latescibacteria” (WS3) – Noha H. Youssef – PLOS ONE

Bioinformatics

BEMOVI, software for extracting behavior and morphology from videos, illustrated with analyses of microbes – Frank Pennekamp – Ecology and Evolution

Techniques

Evaluation of the Ion Torrent Personal Genome Machine for Gene-Targeted Studies Using Amplicons of the Nitrogenase Gene nifH – Bangzhou Zhang – Applied and Environmental Microbiology

Revisiting the Dilution Procedure Used To Manipulate Microbial Biodiversity in Terrestrial Systems – Yan Yan – Applied and Environmental Microbiology

Microbes in the news

How Many Viruses Have Infected You? – Nell GreenfieldBoyce – NPR

A Lifetime of Viruses: Scientists devise an antibody-based test that can generate a person’s complete “viral history” with just one drop of blood. – Amanda B. Keener – The Scientist

Single Test for All Virus Exposure Opens Doors for Researchers – Denise Grady – New York Times

Shielded Microbes Could Spread Life Far Beyond Earth – Elizabeth Howell – Discovery

Unregulated faecal transplants could squander gut-bug promise – New Scientist

Antibiotics affect piglets’ immune system – All About Feed

Good, good, good, good bacteria – Elisabeth Winkler – Sustainable Food Trust

#ASM2015: Many Skin Bacteria Are Dead or Inactive, Study Finds – Health.com

Invasive microbe protects corals from global warming, but at a cost – A’ndrea Elyse Messer, Penn State – Steam Register

Bik’s Picks

India is building millions of toilets. Getting people to use them is a bigger task. – Rama Lakshmi – Washington Post

There Is No Global Warming Hiatus After All – Sarah Zielinski – Smithsonian

New ‘Hellboy’ Dinosaur Unveiled In Scientific Paper With A Romantic Twist – Hilary Hanson – The Huffington Post

Two Newfound Marsupials Do It to Death – Laura Geggel – Discovery

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June 4, 2015

Posted on by

Smoking changes microbial shifts in mouse gut, root microbiome in sugarcane, microbial life after a volcanic eruption, and disturbing developments in the olive bacterial infection situation in Italy.

Human oral microbiome

Phage-bacteria interaction network in human oral microbiome – Jinfeng Wang – Environmental Microbiology

Models of microbiome research

Precision-guided antimicrobial peptide as a targeted modulator of human microbial ecology – Lihong Guo – PNAS USA

Chronic cigarette smoke exposure induces microbial and inflammatory shifts and mucin changes in the murine gut – Liesbeth Allais – Environmental Microbiology

Use of Germ-Free Animal Models in Microbiota-Related Research – Maha Al-Asmakh – Journal of Microbiology and Biotechnology

Animal microbiome

Use of carbon monoxide and hydrogen by a bacteria-animal symbiosis from seagrass sediments – Manuel Kleiner – Environmental Microbiology

Rodent reservoirs of future zoonotic diseases – Barbara A. Han – PNAS

Plant root and soil microbiome

Evolutionary signals of symbiotic persistence in the legume–rhizobia mutualism – Gijsbert D. A. Werner – PNAS

Inner Mongolian steppe arbuscular mycorrhizal fungal communities respond more strongly to water availability than to nitrogen fertilization – Xiaoliang Li – Environmental Microbiology

The core root microbiome of sugarcanes cultivated under varying nitrogen fertiliser application – Yun Kit Yeoh – Environmental Microbiology

Organic matter quantity and source affects microbial community structure and function following volcanic eruption on Kasatochi Island, Alaska – Lydia H. Zeglin – Environmental Microbiology

Water microbiome

Light availability affects stream biofilm bacterial community composition and function, but not diversity – Karoline Wagner – Environmental Microbiology

Bioreactor microbiome

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unraveled with genome-resolved metagenomics – Rose S. Kantor – Environmental Microbiology

Metagenomics

Critical biogeochemical functions in the subsurface are associated with bacteria from new phyla and little studied lineages – Laura A. Hug – – Environmental Microbiology

Combining metagenomics with metaproteomics and stable isotope probing reveals metabolic pathways used by a naturally occurring marine methylotroph – Carolina Grob – Environmental Microbiology

Extrachromosomal circular DNA is common in yeast – Henrik D. Møller – PNAS

More microbes

A noisy linear map underlies oscillations in cell size and gene expression in bacteria –
Yu Tanouchi – Nature

The Matrix Reloaded: How Sensing the Extracellular Matrix Synchronizes Bacterial Communities – Nitai Steinberg and Ilana Kolodkin-Gal – Journal of Bacteriology

Measuring ruggedness in fitness landscapes – Jeremy Van Cleve – PNAS

Microbes in the news

Microbiology: Gut Bacteria cooperate when life gets tough – Université du Luxembourg – Alpha Galileo

Does treating koala chlamydia hurt their gut microbes? – Rachel Feltman – Washington Post

Xylella bacteria increasingly affecting olive trees in Southern Europe – Wageningen UR

Italian scientists vilified in wake of olive-tree deaths: Police investigate researchers’ role in devastating bacterial epidemic – Alison Abbott – Nature

Chemists weigh intact virus mixture with mass spectrometer – Science Daily

Swapping Symbionts Enabled Mediterranean Lichen to Conquer the Arctic – Jennifer Frazer – Scientific American

Researchers explain mechanism that makes their mouthwash so effective against tooth decay – Medical Xpress

Microbes and money

Human Microbiome Market – Global Industry Analysis and Forecast to 2020, by Persistence Market Research – MedGadget

Science, publishing, and career

Retracted gay-marriage study debated at misconduct meet-up: Over rum cocktails at the World Conference on Research Integrity, experts discussed what can be learnt from the fallout of a flawed political-science paper – Richard van Noorden – Nature

Bik’s Picks

Scientists use new ‘tool sled’ to collect sea sponges that have potential to combat various diseases – Science Daily

Groundbreaking study to test metabolism of dugongs to see how much food they need to survive – ABC Australia

Seven new species of miniature frogs discovered (and they’re adorable) – Rachel Feltman – Washington Post

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