Category Archives: Built Environment Microbiology

September 6, 2015

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General microbiome

Recurrent antibiotic exposure may promote cancer formation – Another step in understanding the role of the human microbiota? – Ben Boursi – European Journal of Cancer

Pregnancy and birth microbiome

Clinical chorioamnionitis at term VI: acute chorioamnionitis and funisitis according to the presence or absence of microorganisms and inflammation in the amniotic cavity – Roberto Romero – Journal of Perinatal Medicine

Pregnancy-related changes in the maternal gut microbiota are dependent upon the mother’s periconceptional diet – Wajiha Gohir – Gut Microbes

Potential NICU Environmental Influences on the Neonate’s Microbiome: A Systematic Review – Hartz, Lacey E. – Advances in Neonatal Care

Human oral microbiome

Analysis of the Microbiota of Black Stain in the Primary Dentition – Yue Li – PLOS ONE

Human gut microbiome

Furry pets modulate gut microbiota composition in infants at risk for allergic disease –
Merja Nermes – The Journal of Allergy and Clinical Immunology

Gut microbiome in Chronic Kidney Disease – Maria R. Wing – Experimental Physiology

Editorial: Microbial growth dynamics and human disease – Julia A. Segre – Science

Animal microbiome

Review: Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design – Debby Laukens – FEMS Microbiology Reviews

454 Pyrosequencing-based assessment of bacterial diversity and community structure in termite guts, mounds and surrounding soils – Huxley M. Makonde – Springer Plus

Fish: Study of the microbiome of the intestine of the Comephorus dybowski korotneff, 1904 – N. L. Bel’kova – Ecology

Plant, root, and soil microbiome

An analysis of Pseudomonas genomic diversity in take-all infected wheat fields reveals the lasting impact of wheat cultivars on the soil microbiota – T.H. Mauchline – Environmental Microbiology

Selection of biological indicators appropriate for European soil monitoring – D. Stone – Applied Soil Ecology

Effects of silver nanoparticles on soil microorganisms and maize biomass are linked in the rhizosphere – Wouter Sillen – Soil Biology and Biochemistry

Arbuscular mycorrhiza symbiosis in viticulture: a review – Sophie Trouvelot – Agronomy for Sustainable Development

Soil particle size fractions harbour distinct microbial communities and differ in potential for microbial mineralisation of organic pollutants – Michael Hemkemeyer – Soil Biology and Biochemistry

Differential responses of total and active soil microbial communities to long-term experimental N deposition – Zachary B. Freedman – Soil Biology and Biochemistry

Environmental changes affect the assembly of soil bacterial community primarily by mediating stochastic processes – Ximei Zhang – Global Change

Built environment microbiome

Thesis: The building science of office surfaces: implications for microbial community succession – Mahnaz Zare – University of Toronto

Microbial Ecology

Dynamics of an experimental microbial invasion – Francisco Acosta – PNAS

Click to access 1505204112.full.pdf

Bioinformatics

metaModules identifies key functional subnetworks in microbiome-related disease – Ali May – Bioinformatics

ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data – Jane Hawkey – BMC Genomics

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data – Gregory K. Farrant – BMC Bioinformatics

Inferring microbial interaction network from microbiome data using RMN algorithm
Kun-Nan Tsai – BMC Systems Biology
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September 5, 2015

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Events

The Individual Microbe: Single-cell Analysis and Agent-based Modeling – ASM conference – March 18-20, 2016, Washington DC, USA

R workshop for microbial ecology – Pat Schloss – Nov 2-4, 2015, Detroit – No link but can email Pat at: pschloss@umich.edu

General microbiome

Privacy-Preserving Microbiome Analysis Using Secure Computation – Justin Wagner – BioRxiv

Pregnancy and birth microbiome

Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development – Federica Del Chierico – PLOS ONE

Human oral microbiome

The Effect of Fixed Orthodontic Appliances and Fluoride Mouthwash on the Oral Microbiome of Adolescents – A Randomized Controlled Clinical Trial – Jessica E. Koopman – PLOS ONE

Review: Oral Paleomicrobiology: study of the ancient oral microbiome – Namrata Dagli

Human gut microbiome

The effect of dietary resistant starch type 2 on the microbiota and markers of gut inflammation in rural Malawi children – M. Isabel Ordiz – Microbiome

Gastrointestinal Microbiome Modulator Improves Glucose Tolerance in Overweight and Obese Subjects: A Randomized Controlled Pilot Trial – Candida J. Rebello – Journal of Diabetes and its Complications

Faecal proteomics: A tool to investigate dysbiosis and inflammation in patients with cystic fibrosis – Griet Debyser – Journal of Cystic Fibrosis

Review: Pathways and functions of gut microbiota metabolism impacting host physiology – Smitha Krishnan – Current Opinion in Biotechnology

Review: Microbiome in Inflammatory Arthritis and Human Rheumatic Diseases – Jose U. Scher – Arthritis & Rheumatology

Review: The human microbiome: opportunities and challenges for clinical care – G. B. Rogers – Internal Medicine Journal

Human respiratory microbiome (see also gut microbiome above)

MRSA Colonization and the Nasal Microbiome in Adults at High Risk for Colonization and Infection – Mary T. Bessesen – Journal of Infection

Review: Cystic fibrosis lung microbiome: Opportunities to reconsider management of airway infection – Lindsay J. Caverly – Pediatric Pulmonology

Human other sites

In silico analyses of metagenomes from human atherosclerotic plaque samples – Suparna Mitra – Microbiome

Microbiome models

Distinct Shifts in Microbiota Composition during Drosophila Aging Impair Intestinal Function and Drive Mortality – Rebecca I. Clark – Cell Reports

Perspective: Metabolic labeling puts the microbiome under the microscope – Graham J Britton & Jeremiah J Faith – Nature Medicine

Animal microbiome

The composition of the zebrafish intestinal microbial community varies across development – W Zac Stephens – ISME Journal

Shifts in the Midgut/Pyloric Microbiota Composition within a Honey Bee Apiary throughout a Season – Jane Ludvigsen – Microbes and Environments

The genome of Aiptasia, a sea anemone model for coral symbiosis – Sebastian Baumgarten – PNAS

Special Issue: The Mammalian Microbiome and Its Importance in Laboratory Animal Research – André Bleich and James G. Fox – ILAR Journal

Plant, root, and soil microbiome

Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling – Peter E. Larsen – PLOS ONE

Microbiome change by symbiotic invasion in lichens – Wedin Mats – Environmental Microbiology

Plant-associated microbiomes in arid lands: diversity, ecology and biotechnological potential – Asma Soussi – Plant and Soil

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems – Belinda C. Ferrari – Environmental Microbiology

Water microbiome

Anthropogenic activities drive the microbial community and its function in urban river sediment – Xu Zhang – Journal of Soils and Sediments

Built environment microbiome

Bacterial Communities and Midgut Microbiota Associated with Mosquito Populations from Waste Tires in East-Central Illinois – Chang-Hyun Kim – Journal of Medical Entomology

Hospital’s Hidden Environmental Hazards: Probing the Microbiome – BioScience

Pyrosequencing analysis of bacterial communities in biofilms from different pipe materials in a city drinking water distribution system of East China – Hongxing Ren – Applied Microbiology and Biotechnology

Food microbiology

The genomics of microbial domestication in the fermented food environment –
John G Gibbons – Current Opinion in Genetics & Development

Bioinformatics

Functional Basis of Microorganism Classification – Chengsheng Zhu – PLOS Computational Biology

ReproPhylo: An Environment for Reproducible Phylogenomics – Amir Szitenberg – PLOS Computational Biology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities – Dongwan D. Kang – PeerJ

More Microbiology

Evolution of coexistence in a crowded microplate well – J. Arjan G. M. de Visser – PNAS

The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities – Tomáš Větrovský – Molecular Ecology Resources

Microbes in the news

Microbial diversity insights are often strongly biased – Suffield Times
Small advances: understanding the microbiome – Amanda Smith – ABC Australia

Science, publishing and career

When science fails a scientist – Kim Hunter-Schaedle – Science

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August 30, 2015

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Pregnancy and birth

Fecal Microbial Community Structure Is Stable over Time and Related to Variation in Macronutrient and Micronutrient Intake in Lactating Women – Janae M Carrothers – The Journal of Nutrition

Human oral microbiome

Comparison between Clinical Aspects and Salivary Microbial Profile of Children with and without Early Childhood Caries: A Preliminary Study – Neves AB – Journal of Clinical Pediatric Dentistry

Human gut microbiome

Systematic review: microbial dysbiosis and nonalcoholic fatty liver disease – A. Wieland – Alimentary Pharmacology & Therapeutics

Animal and bioreactor models

Effect of Bifidobacterium thermophilum RBL67 and fructo-oligosaccharides on the gut microbiota in Göttingen minipigs – Sabine A. Tanner – British Journal of Nutrition

Interactions between Drosophila and its natural yeast symbionts—Is Saccharomyces cerevisiae a good model for studying the fly-yeast relationship? – Don Hoang – PeerJ

Differential responses of gut microbiota to the same prebiotic formula in oligotrophic and eutrophic batch fermentation systems – Wenmin Long – Scientific Reports

Animal microbiome

Structure of Manila Clam (Ruditapes philippinarum) Microbiota at the Organ Scale in Contrasting Sets of Individuals – Guillaume Meisterhans – Invertebrate Microbiology

Plant, root, and soil microbiome

Microbiome change by symbiotic invasion in lichens – Wedin Mats – Environmental Microbiology

Comparison of soil microbial communities inhabiting vineyards and native sclerophyllous forests in central Chile – Luis E. Castañeda – Ecology and Evolution

Diversity and distribution of bacterial community in the coastal sediments of Bohai Bay, China – Liping Wang – Acta Oceanologica Sinica

The impact on the soil microbial community and enzyme activity of two earthworm species during the bioremediation of pentachlorophenol-contaminated soils – Zhong Lin – Journal of Hazardous Materials

Water microbiome

Terrestrial origin of bacterial communities in complex boreal freshwater networks – Clara Ruiz-González – Ecology Letters

How are microbial and detrital sources partitioned among and within gastropods species at East Pacific Rise hydrothermal vents? – Sylvie M. Gaudro – Marine Ecology

Extremophile microbiome

Geological connectivity drives microbial community structure and connectivity in polar, terrestrial ecosystems – Belinda C. Ferrari – Environmental Microbiology

Adaptation strategies of endolithic chlorophototrophs to survive the hyperarid and extreme solar radiation environment of the Atacama Desert – Jacek Wierzchos – Frontiers in Microbiology

Microbial biogeography of permafrost thaw ponds across the changing northern landscape – Jérôme Comte – Ecography

Food microbiology

Microbiota of Minas cheese as influenced by the nisin producer Lactococcus lactis subsp. lactis GLc05 – Luana Martins Perin – International Journal of Food Microbiology

Built Environment microbiology

Microbiome interplay: plants alter microbial abundance and diversity within the built environment – Alexander Mahnert – Frontiers in Microbiology

Bioinformatics

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways – Zachary A. King – PLOS Biology

Microbes in the news

Scientists Send Kombucha to Space in Search for Extraterrestrial Life – Kasandra Brabaw – Space.com

How Fats Influence the Microbiome – Kate Yandell – The Scientist

Fish oil diet modifies gut bacteria to boost health – News Medical

Soupy bacteria clogs Missisquoi Bay: “When it rots, it stinks bad” – Joel Banner Baird – Burlington Free Press

Bacteria Hysteria

Caveat: Sponsored by a make-up company. I cannot find any publication associated with this article either. Out of date make-up can contain lethal bacteria, London Met scientist finds – London Metropolitan University

‘There’s no way of knowing what fungus or bacteria is left on it’: Medical expert slams bizarre website that buys USED make-up from beauty lovers – before selling it again – Catherine Townsend – Daily Mail

Science, publishing, and career

The most important tasks for peer reviewers evaluating a randomized controlled trial are not congruent with the tasks most often requested by journal editors – Anthony Chauvin – BMC Medicine
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August 26, 2015

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Microbes in household dust, oropharynx microbiome in schizophrenia, pneumonia in foals, metabolic footprint of bacteria on plant leaves, and Mozzarella cheese.

Human mouth / respiratory microbiome

Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls – Eduardo Castro-Nallar​ – PeerJ

Human vaginal microbiome

Unravelling the Bacterial Vaginosis-Associated Biofilm: A Multiplex Gardnerella vaginalis and Atopobium vaginae Fluorescence In Situ Hybridization Assay Using Peptide Nucleic Acid Probes – Liselotte Hardy – PLOS ONE

Human gut microbiome

Gut feelings of safety: Tolerance to the microbiota mediated by innate immune receptors – Bartlomiej Swiatczak – Microbiology and Immunology

Animal and bioreactor models

The colonic mucus protection depends on the microbiota – Ana M Rodríguez-Piñeiro – Gut Microbes

Sialic acid catabolism drives intestinal inflammation and microbial dysbiosis in mice –
Yen-Lin Huang – Nature Communications

Differential responses of gut microbiota to the same prebiotic formula in oligotrophic and eutrophic batch fermentation systems – Wenmin Long – Scientific Report

Animal microbiome

Composition and Diversity of the Fecal Microbiome and Inferred Fecal Metagenome Does Not Predict Subsequent Pneumonia Caused by Rhodococcus equi in Foals – Canaan M. Whitfield-Cargile – PLOS ONE

Plant, root, and soil microbiome

Metabolic footprint of epiphytic bacteria on Arabidopsis thaliana leaves – Florian Ryffel – The ISME Journal

Diversity of Arbuscular Mycorrhizal Fungi in a Brazilian Atlantic Forest Toposequence – Joice Andrade Bonfim – Microbial Ecology

Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping – Rakesh Santhanam – PNAS

Water microbiome

Marine amoebae with cytoplasmic and perinuclear symbionts deeply branching in the Gammaproteobacteria – Frederik Schulz – Scientific Reports

Built environment microbiome

The ecology of microscopic life in household dust – Albert Barberán – Proceedings B

A Pilot Study on Integrating Videography and Environmental Microbial Sampling to Model Fecal Bacterial Exposures in Peri-Urban Tanzania – Timothy R. Julian – PLOS ONE

Food microbiology

Metabolomics and microbiological profile of Italian mozzarella cheese produced with buffalo and cow milk – Maria Barbara Pisano – Food Chemistry

Microbes in the news

What I Learned From Sequencing the Bacteria in My Apartment – Sarah Zhang – Wired

Thousands of microbes found in house dust – Rebecca Morelle – BBC

Household Dust Packed With Thousands of Microbes – Jennifer Viegas – Discovery

Waikiki Water Tested for Bacteria After Sewage Spill – Caleb Jones – ABC News

Methanotrophs: Could bacteria help protect our environment? – EurekAlert
Is our love affair with antibiotics slowly killing us? – Ailin Quinlan – Independent

Science, publishing, and career

In brief, papers with shorter titles get more citations, study suggests – Dalmeet Singh Chawla

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August 25, 2015

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Microbiome of Polish Cemetery soil, microbiome and risk of Plasmodium infection, interactions between mouse gut microbiota, host Genetics and diet, and the microbiome of air at three different heights.

The microbiome of death

Microbiological Analysis of Necrosols Collected from Urban Cemeteries in Poland – Ireneusz Całkosiński – BioMed Research International

Book: Carrion Ecology, Evolution, and Their Applications – M. Eric Benbow – CRC Press

Pregnancy and birth

Review: Rate of establishing the gut microbiota in infancy has consequences for future health – Shaillay Dogra – Gut Microbes

Editorial with disturbing title: Can establishment of human microbiome be customized after birth with local traditions of first feed and intimate kissing? – Sarman Singh – Journal of Laboratory Physicians

Human oral microbiome

Alterations of the Subgingival Microbiota in Pediatric Crohn’s Disease Studied Longitudinally in Discovery and Validation Cohorts – Judith Kelsen – Inflammatory Bowel Diseases

Review: Human microbiome: From the bathroom to the bedside – Stephen Malnick, Ehud Melzer – World J Gastrointest Pathophysiol

Human gut microbiota / transcriptomics

Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection – Shibu Yooseph – BMC Genomics

Strand-specific community RNA-seq reveals prevalent and dynamic antisense transcription in human gut microbiota – Guanhui Bao – Frontiers in Microbiology

The Fecal Virome of Children with Hand, Foot, and Mouth Disease that Tested PCR Negative for Pathogenic Enteroviruses – Piyada Linsuwanon – PLOS ONE

Review: Gut microbiota and allogeneic transplantation – Weilin Wang – Journal of Translational Medicine

Animal models

Interactions between Gut Microbiota, Host Genetics and Diet Modulate the Predisposition to Obesity and Metabolic Syndrome – Siegfried Ussar – Cell Metabolism

Physical Activity Differentially Affects the Cecal Microbiota of Ovariectomized Female Rats Selectively Bred for High and Low Aerobic Capacity – Tzu-Wen Liu – PLOS ONE

Animal microbiome

Isolation of oxalotrophic bacteria associated with Varroa destructor mites – M. Maddaloni – Letters in Applied Microbiology

Diversity of bacterial communities in the midgut of Bactrocera cucurbitae (Diptera: Tephritidae) populations and their potential use as attractants – Ashok B. Hadapad – Pest Management Science

Midgut bacterial communities in the giant Asian honeybee (Apisdorsata) across four developmental stages: a comparative study – Prakaimuk Saraithong – Insect Science

Bacterial communities associated with four ctenophore genera from the German Bight (North Sea) – Wenjin Hao – FEMS Microbial Ecology

Plant, root, and soil microbiome
(also see study above filed under Microbiome of Death)

The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon – Wei H. Xu – Frontiers in Microbiology

Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil – Yendi E. Navarro-Noya – Archaea

Molecular characterization of microbial communities in the rhizosphere soils and roots of diseased and healthy Panax notoginseng – Zhaoxiang Wu – Antonie van Leeuwenhoek

The diversity changes of soil microbial communities stimulated by climate, soil type and vegetation type analyzed via a functional gene array – Fu Chen – World Journal of Microbiology and Biotechnology

Water microbiome

Carbon fixation by basalt-hosted microbial communities – Beth N. Orcutt – Frontiers in Microbiology

Annual dynamics of North Sea bacterioplankton: Seasonal variability superimposes short-term variation – Judith Lucas – Microbiology Ecology

Ecology and Distribution of Thaumarchaea in the Deep Hypolimnion of Lake Maggiore –
Manuela Coci – Archaea

Viral and grazer regulation of prokaryotic growth efficiency in temperate freshwater pelagic environments – A.S. Pradeep Ram – FEMS Microbiology Ecology

Air / built environment microbiome

Vertical distribution of airborne bacterial communities in an Asian-dust downwind area, Noto Peninsula – Teruya Maki – Atmospheric Environment

Microbiological consequences of indoor composting – Alexandre Naegele – Indoor Air

Extremophiles

Response of the rare biosphere to environmental stressors in a highly diverse ecosystem (Zodletone spring, OK, USA) – Suzanne Coveley – PeerJ

Food microbiology

Wine fermentation microbiome: a landscape from different Portuguese wine appellations – Cátia Pinto – Frontiers in Microbiology

Difference of microbial community stressed in artificial pit muds for Luzhou-flavour liquor brewing revealed by multiphase culture-independent technology – Liqiang Zhang – Journal of Applied Microbiology

Monitoring of Yeast Communities and Volatile Flavor Changes During Traditional Korean Soy Sauce Fermentation – Young-Ran Song – Journal of Food Science

Bioreactor microbiology

Microbial community in a hydrogenotrophic denitrification reactor based on pyrosequencing – Hongyu Wang – Applied Microbiology and Biotechnology

Techniques and other microbiology

Application of iChip to Grow “Uncultivable” Microorganisms and its Impact on Antibiotic Discovery – Rinzhin T. Sherpa – Journal of Pharmacy & Pharmaceutical Sciences

Cultivating the uncultured: growing the recalcitrant cluster-2 Frankia strains – Maher Gtari – Scientific Reports

Isolation of Genetically Tractable Most-Wanted Bacteria by Metaparental Mating – Páraic Ó Cuív – Scientific Reports

Burkholderia bacteria infectiously induce the proto-farming symbiosis of Dictyostelium amoebae and food bacteria – Susanne DiSalvo – PNAS

Science, publishing, and career

A call to arms for women in science – Women’s Agenda
Microbes in the news

The Bacteria That Turn Amoebas Into Farmers – Ed Yong – National Geographic

Testers find twice as many ‘superbugs’ in conventional hamburger as organic ones – Lena H. Sun – Washington Post

Humans carry more antibiotic-resistant bacteria than animals they work with – Medical Xpress
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August 19, 2015

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Guidelines and principles to use “holobionts”, microbiome and provoking autoimmunity in uveitis, bacteria in confiscated passerines, and ecology of the Miscellaneous Crenarchaeotic Group archaea.

General microbiome

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes – Seth R. Bordenstein , Kevin R. Theis – PLOS Biology

Human eye microbiome

Uveitis (Eye): Microbiota-Dependent Activation of an Autoreactive T Cell Receptor Provokes Autoimmunity in an Immunologically Privileged Site – Reiko Horai – Immunity

Human gut microbiome

Review: Diagnostic and Prognostic Microbial Biomarkers in IBD – Marla Dubinsky – Gastroenterology

Letter to the editor: Can inflammatory bowel disease really be solved by the multiple -omics and meta-omics analyses? – Xiaofa Qin – Immunology Letters

Animal models

In vivo imaging and tracking of host–microbiota interactions via metabolic labeling of gut anaerobic bacteria – Naama Geva-Zatorsky – Nature Medicine

Associative patterns among anaerobic fungi, methanogenic archaea, and bacterial communities in response to changes in diet and age in the rumen of dairy cows – Sanjay Kumar – Frontiers in Microbiology

Diet- and Genetically-Induced Obesity Differentially Affect the Fecal Microbiome and Metabolome in Apc1638N Mice – Anna C. Pfalzer – PLOS ONE

Animal microbiome

Detection of bacteria and fungi and assessment of the molecular aspects and resistance of E. coli isolated from confiscated passerines intended for reintroduction programs – Patricia Braconaro – Microbial Pathogenesis

Mining of luxS genes from rumen microbial consortia by metagenomic and metatranscriptomic approaches – Ines Ghali – Animal Science Journal

Isolation and identification of marine fish tumour (odontoma) associated bacteria – Ramalingam Vijayakumar – Journal of Coastal Life Medicine

A facultative endosymbiont in aphids can provide diverse ecological benefits – E. R. Heyworth andJ. Ferrari – Journal of Evolutionary Biology

Not sure why a study on RNAseq and 16S rRNA PCR on voles in France was published in PLOS NTD: A Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife – Maria Razzauti – PLOS Neglected Tropical Diseases

Plant, roots, and soil microbiome

Assembly of Active Bacterial and Fungal Communities Along a Natural Environmental Gradient – Rebecca C Mueller – Microbial Ecology

Effects of imidacloprid on soil microbial communities in different saline soils– Qingming Zhang – Environmental Science and Pollution Research

Water microbiome

Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula – Jeff S. Bowman – PLOS ONE

Diazotrophic bacterial community variability in a subtropical deep reservoir is correlated with seasonal changes in nitrogen – Lina Wang – Environmental Science and Pollution Research

Built environment microbiome

Assessment of contamination using an ATP bioluminescence assay on doorknobs in a university-affiliated hospital in Japan – Naoko Kajigaya – BMC Research Notes

Diversity and antibiotic resistance profiles of Pseudomonads from a hospital wastewater treatment plant – D.O. Santoro – Journal of Applied Microbiology

Cleanroom Maintenance Significantly Reduces Abundance but Not Diversity of Indoor Microbiomes – Alexander Mahnert – PLOS ONE

Archaea

Insights in the ecology and evolutionary history of the Miscellaneous Crenarchaeotic Group lineage – Mireia Fillol – ISME Journal

Metabolomics

Plasma metabolomic profiles enhance precision medicine for volunteers of normal health –
Lining Guo – PNAS

Techniques

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome – Luigi Faino – mBio

Microbes in the news

Bacteria’s secret weapon against pesticides and antibiotics revealed – Aarhus University – EurekAlert

Die, Bacteria! Engineered particles deliver targeted antibiotics – Helen Knight – Technology Review

Bacteria with synthetic DNA create protein never found in Nature – For when the usual four nucleotides can’t give you what you want – Alexandra Ossola – PopSci

Second Plague Case Traced to Yosemite National Park – Maggie Fox – NBC News

Science, publishing, and career

Increasing disparities between resource inputs and outcomes, as measured by certain health deliverables, in biomedical research – Anthony Bowena and Arturo Casadevall – PNAS
Return on Investment Slipping in Biomedical Research – Johns Hopkins Bloomberg School of Public Health

Science Week Australia: UNSW moves to strengthen women’s role in science – Marcus Strom – Sydney Morning Herald

Bik’s Picks

Stanford’s Angel of Grief Statue Has Arm Chopped Off By Vandals: The arm, made of fine Italian marble, is worth an estimated $20,000 – NBC Bay Area

Hummingbird tongues are way weirder than we thought – Rachel Feltman – Washington Post

Can’t go to Mars? At least sign the card – Jillian Kestler-D’Amours – The Star

Flying Spiders Found—and They Can Steer in Mid-Air – Traci Watson – National Geographic

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August 16, 2015

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So many new papers, that I need to do a Sunday post as well. Human nose microbiota changes during rhinovirus infection. tsrimethylamine and human gut microbiome, gut microbiota in sloths, and effect of timber harvesting on forest soils.

Human oral microbiome

Long-term evaluation of the antimicrobial susceptibility and microbial profile of subgingival biofilms in individuals with aggressive periodontitis – Talita Gomes Baêta Lourenco – Brazilian Journal of Microbiology

The human oral metaproteome reveals potential biomarkers for caries disease – Pedro Belda-Ferre – Proteomics

Human respiratory microbiome

Changes in microbiota during experimental human Rhinovirus infection – J. J. Hofstra – BMC Infectious Disease

Human gut microbiome

The Microbiome and Osteosarcopenic Obesity in Older Individuals in Long-Term Care Facilities – Julia E. Inglis – Current Osteoporosis Reports

Review: Microbiology Meets Big Data: The Case of Gut Microbiota–Derived Trimethylamine – Gwen Falony – Annual Review of Microbiology

Review: Gut microbiota modulate the immune effect against hepatitis B virus infection – D. Xu – European Journal of Clinical Microbiology & Infectious Diseases

Microbiome models

Osteopontin Deficiency Accelerates Spontaneous Colitis in Mice with Disrupted Gut Microbiota and Macrophage Phagocytic Activity – Takahiko Toyonaga – PLOS ONE

Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice – Kirsty Brown – ISME Journal

Prebiotic effects of diet supplemented with the cultivated red seaweed Chondrus crispus or with fructo-oligo-saccharide on host immunity, colonic microbiota and gut microbial metabolites – Jinghua Liu – BMC Complementary and Alternative Medicine

Animal microbiome

Metagenome Sequencing of the Greater Kudu (Tragelaphus strepsiceros) Rumen Microbiome – Anita N. Dube – Genome Announcements

Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths – Kimberly A. Dill-McFarland – Environmental Microbiology

Microbiome Variation Across Amphibian Skin Regions: Implications for Chytridiomycosis Mitigation Efforts – Arnaud Bataille – Microbial Ecology

Plant, root, and soil microbiome

Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from Northern Australia – Alyssa M. Cornall – Environmental Toxicology and Chemistry

Response of Archaeal and Bacterial Soil Communities to Changes Associated with Outdoor Cattle Overwintering – Alica Chroňáková – PLOS ONE

Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils – Hilary T C Leung – ISME Journal

Microbial Community Composition and Extracellular Enzyme Activities Associated with Juncus roemerianus and Spartina alterniflora Vegetated Sediments in Louisiana Saltmarshes – Anthony J. Rietl – Microbial Ecology

Water microbiome

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time-series and global field samples – Alma Parada – Environmental Microbiology

Diversity of Synechococcus at the Martha’s Vineyard Coastal Observatory: Insights from Culture Isolations, Clone Libraries, and Flow Cytometry – Kristen R. Hunter-Cevera – Microbial Ecology

Built environment microbiome

The Effectiveness of Three Home Products in Cleaning and Disinfection of S. aureus and E. coli on Home Environmental Surfaces – Nancy Goodyear – Journal of Applied Microbiology

Geochemical influences and mercury methylation of a dental wastewater microbiome – Asha Rani – Scientific Reports

Metagenomics

Research Highlights: An encrypted growth signature – Naomi Attar – Nature Reviews Microbiology

Archaea / Metabolomics

Untargeted metabolomics studies employing NMR and LC–MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis – Timothy Hamerly – Metabolomics

Microbes in the news

Toxoplasma parasite’s greedy appetite may be its downfall – University of Melbourne – EurekAlert

Let’s hope the stock photo was not related to the techniques used in this study:
Computerized ‘fishing expedition’ hooks 12,500 virus genomes – Brooks Hays – UPI

New Beach Act aims for faster results on bacteria tests – Dan Radel – APP.com

Swedish infant infects four others with resistant bacteria – New Straits Times

What’s lurking in your lungs? Surprising findings emerge from U-M microbiome research – Health Canal

Science, publishing, and career

Fixing the Leaky Bucket: What Tech Companies Must Do to Retain Their Best Female Talent – Belle Beth Cooper – Huffington Post

Bik’s Picks

Here’s How To Call The International Space Station – Gizmodo

Playing Tetris for 3 minutes could reduce your worst cravings – IBN Live

Teenagers are making themselves DIY braces and it is horrifying – Amy Willis – Metro.co.uk

How the internet of things is having an impact in Africa – HTXT Africa

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August 12, 2015

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Drug metabolism by gut microbiota, nature vs. nurture in inbred strains of mice, gnotobiotic Drosophila, bat virome, and influence of protist predation on marine microbiomes.

General microbiome

Short-chain fatty acids in control of body weight and insulin sensitivity – Emanuel E. Canfora – Nature Reviews Endocrinology

Pregnancy and birth microbiome

Streptococcal Diversity of Human Milk and Comparison of Different Methods for the Taxonomic Identification of Streptococci – Virginia Martín – Journal of Human Lactation

Human gut microbiome

Editorial: Drug Metabolism by the Host and Gut Microbiota: A Partnership or Rivalry?
Hollie I Swanson – Drug Metabolism and Disposition
Review: Mechanisms of How the Intestinal Microbiota Alters the Effects of Drugs and Bile Acids – Curtis D. Klaassen – Drug Metabolism and Disposition

Comparison of the gut microbiota composition between obese and non-obese individuals in a Japanese population, as analyzed by terminal restriction fragment length polymorphism and next-generation sequencing – Chika Kasai – BMC Gastroenterology

Animal and other models

Microbiota in 110 diverse inbred strains of mice: Genetic and environmental control of host-gut microbiota interactions – Elin Org – Genome Research

Co-culturing Escherichia coli O157:H7 with a non-pathogenic E. coli strain increases toxin production and virulence in a germ-free mouse model – Kakolie Goswami – Infection and Immunity

Ovariectomy results in differential shifts in gut microbiota in low versus high aerobic capacity rats – Kimberly A. Cox-York – Physiological Reports

Studying host-microbiota mutualism in Drosophila: Harnessing the power of gnotobiotic flies – Dali Ma – Biomedical Journal

MyD88 Signaling Regulates Steady-State Migration of Intestinal CD103+ Dendritic Cells Independently of TNF-α and the Gut Microbiota – Karin Hägerbrand – The Journal of Immunology

Animal microbiome

Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases – Zhiqiang Wu – ISME Journal

Plant, root, and soil microbiome

Host promiscuity in symbiont associations can influence exotic legume establishment and colonization of novel ranges – Metha M. Klock – Diversity and Distributions

Temporal and spatial influences incur reconfiguration of Arctic heathland soil bacterial community structure – Richard Hill – Environmental Microbiology

Water microbiome

Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions – Federico Baltar – ISME Journal

Waste and water treatment microbiology

The activated sludge ecosystem contains a core community of abundant organisms – Aaron M Saunders – ISME Journal

Core-satellite populations and seasonality of water meter biofilms in a metropolitan drinking water distribution system – Fangqiong Ling – ISME Journal

More microbes

Levels and limits in artificial selection of communities – Manuel Blouin – Ecology Letters

Editorial: Origin of the Yeast Whole-Genome Duplication – Kenneth H. Wolfe – PLOS Biology
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker’s Yeast Lineage – Marina Marcet-Houben – PLOS Biology

Microbes in the news

Global Human Microbiome Market: Asia is expected to show high growth rates by 2020 – MedGadget

Things I Tell My Mom: Five ways for you to participate in science – Cathy Seiler – Ahwatukee Foothills News

Why making and taking fermented drinks is becoming popular again – John McKenna – The Irish Times

Protein Goes Green: Can Algae Become The Next Soy? – Jessie Rack – NPR

Cultured Coffee offers the flavor of poop-brewed coffee without the crap – TJ Dietsch – Geek

Making kefir at home is easy, healthy – Kit Waskom Pollard – Baltimore Sun

‘Genomic Archaeology’ Reveals That Lager Yeast Was Born More Than Once – Andrea Alfano -Tech Times

Researchers resurrect extinct virus to use for gene therapy: Evolutionary ancestors remade based on current viruses – Ars Technica

Science, publishing, and career

Make Peer Review Public: How to make science faster and more robust – Adam Marcus and Ivan Oransky – Slate

Despite concerted effort, barriers to women in science remain – Jennifer Ann Thomson – The Conversation

Outreach: Primary School outreach – inspiring young minds with science – Mariya Lobanovska – SGM

Physics: She did it all: Val Gibson enjoys the autobiography of Mary K. Gaillard, the first female physics professor at Berkeley – Val Gibson – Nature

Bik’s Picks

Octopus Genome Offers Insights Into One Of Ocean’s Cleverest Oddballs – Nell Greenfieldboyce – NPR

Meteor time! How to watch the big Perseid shower – Paul Rogers – San Jose Mercury News

MIT tackling more serious science: they program beer-delivering robots – ZME Science

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August 8, 2015

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Lung and oral microbiomes in setting of HIV infection, cell biology of the plant–microbe interface, deep see prokaryotes, bacterial succession during grape fermentation, and correcting amplicon errors with Dada2.

Pregnancy and birth microbiome

Is abnormal vaginal microflora a risk factor for intrauterine fetal growth restriction? – Natalija Vedmedovska – Asian Pacific Journal of Reproduction

Multiple Opportunistic Pathogens, but Not Pre-existing Inflammation, May Be Associated with Necrotizing Enterocolitis – Steven T. Leach – Digestive Diseases and Sciences

Review: Nutrient availability, the microbiome and intestinal transport during pregnancy – Stuart Astbury – Applied Physiology, Nutrition, and Metabolism

Human oral and lung microbiome

Multi-center Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals – James M. Beck – American Journal of Respiratory and Critical Care Medicine

Review: Microbial protection and virulence in periodontal tissue as a function of polymicrobial communities: symbiosis and dysbiosis – Frank A. Roberts and Richard P. Darveau – Periodontology 2000

Needs assessment for emerging oral microbiome knowledge in dental hygiene education – R. Constance Wiener – Journal of Epidemiological Research

Human reproductive microbiome

Is abnormal vaginal microflora a risk factor for intrauterine fetal growth restriction? – Natalija Vedmedovska – Asian Pacific Journal of Reproduction

Human gut microbiome

Alterations of mucosal microbiota in the colon of patients with inflammatory bowel disease revealed by real time polymerase chain reaction amplification of 16S ribosomal ribonucleic acid – Jayakanthan Kabeerdoss – Indian J Med Res

An In Vitro Method to Assess Soil Arsenic Metabolism by Human Gut Microbiota: Arsenic Speciation and Distribution – Naiyi Yin – Environmental Science & Technology

Review: Does a low FODMAP diet help IBS? – Drug and Therapeutics Bulletin

Microbiome models

Modulation of intestinal microbiota in mice by kefir administration – Dong-Hyeon Kim – Food Science and Biotechnology

High nutrient availability reduces the diversity and stability of the equine caecal microbiota – Naja C. K. Hansen – Microbial Ecology in Health & Disease

Impact of Dietary Fiber/Starch Ratio in Shaping Cecal Microbiota in Rabbits – YanLi Zhu – Canadian Journal of Microbiology

Animal microbiome

Electrical Retrieval of Living Microorganisms from Cryopreserved Marine Sponges Using a Potential-Controlled Electrode – Sumihiro Koyama – Marine Biotechnology

PhD Thesis: Reproduction, Sex Ratio and Bacterial Communities of the Coffee Berry Borer Hypothenemus Hampei F. (Coleoptera: Curculionidae) – Mariño Cárdenas – Universidad de Puerto Rico

Effect of starch source (corn, oats or wheat) and concentration on fermentation by equine fecal microbiota in vitro – Brittany E. Harlow – Journal of Applied Microbiology

Role of peptidases of the intestinal microflora and prey in temperature adaptations of the digestive system in planktivorous and benthivorous fish – V. V. Kuz’mina – Fish Physiology and Biochemistry

Plant, root, and soil microbiome

Environmental conditions rather than microbial inoculum composition determine the bacterial composition, microbial biomass and enzymatic activity of reconstructed soil microbial communities – Weibing Xun – Soil Biology and Biochemistry

Editorial: Introduction to a Virtual Special Issue on cell biology at the plant–microbe interface – Ralph Panstruga and Hannah Kuhn – New Phytologist

Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China – Jing Zhou – Soil Biology and Biochemistry

Functional and structural responses of methanogenic microbial communities in Uruguayan soils to intermittent drainage – Yang Ji – Soil Biology and Biochemistry

Effects of pasture management on soil fertility and microbial communities in the semi-arid grasslands of Inner Mongolia – Jun Liu – Journal of Soils and Sediments

Antibiotic resistance differentiates Echinacea purpurea endophytic bacterial communities with respect to plant organs – Alessio Mengoni – Research in Microbiology

Effect of combined microbes on plant tolerance to Zn–Pb contaminations – Anna Ogar – Environmental Science and Pollution Research

From mesophilic to thermophilic digestion: the transitions of anaerobic bacterial, archaeal, and fungal community structures in sludge and manure samples – Weimin Sun – Applied Microbiology and Biotechnology

Water microbiome

Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites – Aurélien Saghaï – Frontiers in Microbiology

Thesis: Geobiological interactions of archaeal populations in acidic and alkaline geothermal springs of Yellowstone National Park, WY, USA – Jacob Preston Beam – Montana State University

Global diversity and biogeography of deep-sea pelagic prokaryotes – Guillem Salazar – ISME Journal

Built environment microbiology

Halophilic microbial communities in deteriorated buildings – Justyna Adamiak – World Journal of Microbiology and Biotechnology

Food microbiology

Insights into the bacterial community and its temporal succession during the fermentation of wine grapes – Hailan Piao – Frontiers in Microbiology

Identification of key microorganisms involved in Douchi fermentation by statistical analysis and their use in an experimental fermentation – Chen Chen – Journal of Applied Microbiology

In vitro fermentation of lupin seeds (Lupinus albus) and broad beans (Vicia faba): dynamic modulation of the intestinal microbiota and metabolomic output – Patricia Gullón – Food & Function

Bioinformatics

DADA2: High resolution sample inference from amplicon data – Benjamin J Callahan

Transcriptomics

Molecular and chemical dialogues in bacteria-protozoa interactions – Chunxu Song – Scientific Reports

Techniques

Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool – Monika A. Gorzelak – PLOS ONE

Microbes in the News

Prestigious Japanese university comes up with cheesecake … made with Gorilla bacteria! – RocketNews

Lambton College research project proves successful in eliminating bacteria in firefighting gear – Lambton College

Where the sausage gets made – Holly Ganz – MicroBEnet

Calgary diseases expert on the importance of studying our guts – The Globe and Mail

Bik’s Picks

Creepers’ peepers: Why animals’ pupils have different shapes – Nicholas St. Fleur – Seattle Times

Venomous frogs discovered during painful scientific mishap: Frogs head-butt enemies with their spines to inject toxic venom – CBC News

ISS Astronauts to Sample Leafy Greens Grown on Space Station – NDTV

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August 3, 2015

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Comparing bifidobacterial strains from mom and baby using metagenomics, finding good markers for human fecal matter, the microbiome of a meat processing facility, and a review on community assembly.

Pregnancy and birth microbiome

Metagenomics: Exploring vertical transmission of bifidobacteria from mother to child – Christian Milani – Applied and Environmental Microbiology

Animal microbiome

Comparison of sewage and animal fecal microbiomes using oligotyping reveals potential human fecal indicators in multiple taxonomic groups – Jenny C. Fisher – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Nitrogen Cycling Potential of a Grassland Litter Microbial Community – Michaeline B. Nelson – Applied and Environmental Microbiology

Water microbiome

Impact of silver nanoparticles on benthic prokaryotes in heavy metal-contaminated estuarine sediments in a tropical environment – B. Antizar-Ladislao – Marine Pollution Bulletin

Built environment and food microbiology

Meat processing plant microbiome and contamination patterns of cold-tolerant bacteria causing food safety and spoilage risks in the manufacture of vacuum-packaged, cooked sausages – Jenni Hultman – Applied and Environmental Microbiology

Microbial Ecology

An Economic Framework of Microbial Trade – Joshua Tasoff – PLOS ONE

Review: Historical Contingency in Community Assembly: Integrating Niches, Species Pools, and Priority Effects – Tadashi Fukami – Annual Review of Ecology, Evolution, and Systematics

Microbes in the news

These Bizarre Fungi Resemble Corpse Fingers, UFOs, Tongues – Liz Langley – National Geographic

Alarming survey of NYC subway bacteria gets corrected – CBS News

WHO and Sailing Body Seek Virus Tests in Rio Olympic Venues – Stephen Wade – ABC News

Grocers Are Taking Their Anti-Antibiotic Stance to the High Seas:Costco will buy more farmed salmon from Norway, which is raised with far fewer drugs than Chilean fish. – Willy Blackmore – Take Part

There may be a complex market living in your gut: Researchers apply economic concepts to explore the mysteries of the microbial world – Science Daily

Alum helps ASU microbiology students realize their dreams – Arizona State University

India’s Youngest PG To Do Doctorate In Environmental Microbiology – Tehelka

Bacteria pieces in Royal Jelly: No shot needed, bees vaccinate their babies naturally – Arizona State University

Science, publishing, and career

The silent revolution in peer review – The Loop – Frontiers

Bik’s Picks

Women’s immune system genes operate differently from men’s – Stanford Medicine

Study Shows Plants Exhibit ‘Animal-Like’ Signals Despite Lack Of Nervous System – Rhodi Lee – Tech Times

Florida’s giant snails prove to be a slippery foe: Plant detectives and Sierra, the lab, are on their trail – AFP News