Category Archives: Microbes in the News

August 27, 2015

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Microbiome general/other

A comprehensive repertoire of prokaryotic species identified in human beings – Perrine Hugon – The Lancet Infectious Diseases

Linking the relevance of microbiota composition shifts with intestinal health disorders: a complex issue – Filip Boyen – Veterinary Journal

Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes – Shira R. Abeles – PLOS ONE

High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis– Aicui Liu – Drug Des Devel Ther

Pregnancy and birth microbiome

Several abstracts in Placenta:

 

Human oral microbiome

Pyrosequencing analysis of apical microbiota of teeth with persistent apical periodontitis – Yifan Ping – Journal of Dental Sciences

Human gut microbiome

Structure and function of the healthy pre-adolescent pediatric gut microbiome – Emily B. Hollister – Microbiome

Are proton pump inhibitors affecting intestinal microbiota health? – S. Melgar – Gastroenterology

Microbiome models

Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling – Robert Caesar – Cell Metabolism

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development – Adam R Burns – The ISME Journal

Animal microbiome

The microbial community structure of the cotton rat nose – Diego Chaves-Moreno – Environmental Microbiology Reports

Water / Extremophile microbiome

Freshwater ice as habitat: partitioning of phytoplankton and bacteria between ice and water in central European reservoirs – Robert M.L. McKay – Environmental Microbiology Reports

High protists diversity in the plankton of sulfurous lakes and lagoons examined by 18s rRNA gene sequence analyses – Xavier Triadó-Margarit – Environmental Microbiology Reports

Bioreactor microbiology

Housefly Larvae Vermicomposting Efficiently Attenuates Antibiotic Resistant Genes in Swine Manure Coupled with Distinct Bacterial Population Change – Hang Wang – Applied and Environmental Microbiology

Techniques

A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing – Wenke Smets – PeerJ PrePrints

Mock communities highlight the diversity of host-associated eukaryotes – Laura Wegener Parfrey – Molecular Ecology

Microbes in the news

Lab experiments question popular measure of ancient ocean temperatures – Hannah Hickey – University of Washington

Is your spacecraft contaminating the universe? – Jonathan Eisen – Microbe.net

Birmingham Zoo closes aviary after bacteria found in bird – Washington Times

Science, publishing, and career

EntryPoint! places students with disabilities on STEM tracks – Becky Ham – Science

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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 22, 2015

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The microbiology of pig carcasses in streams, machine learning classifiers and bacterial vaginosis, and chestnut leaf extracts inhibiting Staphylococcus aureus growth.

Microbiome of death

The Potential of High-throughput Metagenomic Sequencing of Aquatic Bacterial Communities to Estimate the Postmortem Submersion Interval – Mark Eric Benbow – Journal of Forensic Sciences

Pregnancy and birth

Machine learning classifiers provide insight into the relationship between microbial communities and bacterial vaginosis – Daniel Beck – Biodata Mining

Review: Congenital Chagas disease as an ecological model of interactions between Trypanosoma cruzi parasites, pregnant women, placenta and fetuses – Yves Carlier – Acta Tropica

Animal models

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development – Adam R Burns – The ISME Journal

Plant, root, and soil microbiome

Editorial: Plant microbiome blueprints – Cara H. Haney – Science

Castanea sativa (European Chestnut) Leaf Extracts Rich in Ursene and Oleanene Derivatives Block Staphylococcus aureus Virulence and Pathogenesis without Detectable Resistance – Cassandra L. Quave – PLOS ONE

Water microbiome

Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics – Jennifer R. Brum – The ISME Journal

Experimental insights into the importance of aquatic bacterial community composition to the degradation of dissolved organic matter – Jürg B Logue – The ISME Journal

Microbes in the news

Chestnut leaves yield extract that disarms deadly staph bacteria – Phys.org

TSRI Scientists Discover Mechanism Behind Antibiotic-Resistance In Bacteria – Guneet Bhatia – IBD Times

King of fermentation brings together microbiology, food & community – Shady Grove Oliver – KTOO

Science, publishing and career

The Hidden Bias of Science’s Universal Language: The vast majority of scientific papers today are published in English. What gets lost when other languages get left out? – Adam Huttner-Koros – The Atlantic

Bik’s Picks

Minneapolis woman is raising 400 monarch butterflies in her home – Aimee Blanchette – Star Tribune

Climate Change To Blame For Dogs’ Evolution From Cats – J.R. Duren – Immortal

Google Chrome spellchecks multiple languages at once – Steve Dent – Engadget

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August 20, 2015

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Jobs

Jobs at Technical University of Denmark: Three PhD scholarships at the interface of synthetic biology, metagenomics and bacterial evolution

Pregnancy and birth

The Placental Microbiome Varies in Association with Low Birth Weight in Full-Term Neonates – Jia Zheng – Nutrients

Impact of mode of delivery on the milk microbiota composition of healthy women – R. Cabrera-Rubio – Journal of Developmental Origins of Health and Disease

Human oral microbiome

Dental plaque as a biofilm and a microbial community – implications for treatment – P.D. Marsh – Journal of Oral Biosciences

Human gut microbiome

Low Level Engraftment and Improvement following a Single Colonoscopic Administration of Fecal Microbiota to Patients with Ulcerative Colitis – Christopher J. Damman – PLOS ONE

The presence of Oxalobacter formigenes in the microbiome of healthy young adults – Clea Barnett – The Journal of Urology

The gut microbial community in metabolic syndrome patients is modified by diet – Carmen Haro – The Journal of Nutritional Biochemistry

Review: Intestinal Microbiota and Celiac Disease: Cause, Consequence or Co-Evolution? – María Carmen Cenit – Nutrients

Review: The intestinal microbiome in human disease and how it relates to arthritis and spondyloarthritis – Mary-Ellen Costello – Best Practice & Research Clinical Rheumatology

Editorial: Getting Healthier Through Microbiome Makeover – Duc Hong Le – EBioMedicine

Review: Nutritional Modulation of Gut Microbiota – The Impact on Metabolic Disease Pathophysiology – Patricia Ojeda – The Journal of Nutritional Biochemistry

Animal models

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

IL-21 and probiotic therapy improve Th17 frequencies, microbial translocation, and microbiome in ARV-treated, SIV-infected macaques – A M Ortiz – Mucosal Immunology

Animal microbiome

The rectal microbiota of cats infected with feline immunodeficiency virus infection and uninfected controls – JS Weese – Veterinary Microbiology

Bartonella Infection among Cats Adopted from a San Francisco Shelter, Revisited – Drew A. Fleischman – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter – Lucia Žifčáková – Environmental Microbiology

Diversity and complexity of microbial communities from a chlor-alkali tailings dump – Cyril Zappelini – Soil Biology and Biochemistry

Different impacts of native and exotic earthworms on rhizodeposit carbon sequestration in a subtropical soil – Jinhua Huang – Soil Biology and Biochemistry

Polycyclic aromatic hydrocarbons degradation and microbial community shifts during co-composting of creosote-treated wood – Stefano Covino – Journal of Hazardous Materials

Waste microbiology

Occurrence of and Sequence Variation among F-Specific RNA Bacteriophage Subgroups in Feces and Wastewater of Urban and Animal Origins – C. Hartard – Applied and Environmental Microbiology

Pathogenic Enteric Viruses and Microbial Indicators during Secondary Treatment of Municipal Wastewater – Naim Montazeri – Applied and Environmental Microbiology

Metaproteomics of activated sludge from a wastewater treatment plant – A pilot study – Sebastian Püttker – Proteomics

Food microbiology

Chromosomal Copy Number Variation in Saccharomyces pastorianus Is Evidence for Extensive Genome Dynamics in Industrial Lager Brewing Strains – M. van den Broek – Applied and Environmental Microbiology

Not sure why the title is between quotes: “Spoilage of vacuum-packed beef by the yeast Kazachstania psychrophila” – Jan Kabisch – 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

Microbes in the news

Does This Phylum Make Me Look Fat? – Katherine Harmon Courage – NPR

Stanford researchers find surprising level of tick-borne disease risk on local trails – Rob Jordan

What Gut Bacteria Can Teach Us About Eating Disorders: uBiome and University of North Carolina Launch Groundbreaking Study – Global News Wire

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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 18, 2015

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New paper from our lab about human microbiota during pregnancy, association between obesity and cervical microflora, Argentina soil metagenomes, proteomics library, and microbiology during mozzarella cheese making.

Events and conferences

ECCMID: 26th European Congress of Clinical Microbiology and Infectious Diseases: April 2016, Istanbul, Turkey

General microbiome

Review: Fulfilling the Promise of Microbiomics to Revolutionize Medicine – Traci L Testerman – J Microbiol Exp

Review: Cross-kingdom similarities in microbiome functions – Rodrigo Mendes – ISME Journal

Pregnancy and birth microbiome

From our lab: Temporal and spatial variation of the human microbiota during pregnancy – Daniel B. DiGiulio – PNAS

Maternal group B Streptococcus and the infant gut microbiota – A. E. Cassidy-Bushrow – Journal of Developmental Origins of Health and Disease

The stool microbiota of insulin resistant women with recent gestational diabetes, a high risk group for type 2 diabetes – Marina Fugmann – Scientific Reports

Human reproductive tract microbiome

Relationship of Specific Bacteria in the Cervical and Vaginal Microbiotas With Cervicitis – Linda M. Gorgos – Sexually Transmitted Diseases

Changes in vaginal microbiota following antimicrobial and probiotic therapy – Jean M. Macklaim – Microbial Ecology in Health and Disease

Association between obesity and cervical microflora dominated by Lactobacillus iners in Korean women – Hea Young Oh – Journal of Clinical Microbiology

Distribution of human papillomavirus (HPV) genotypes and bacterial vaginosis presence in cervical samples from Paraguayan indigenous – Pamela Mongelos – International Journal of Infectious Diseases

The most common isolated microorganisms and its clinical manifestation in hospitalised women suffering from urogenital diseases in Latvia – Anatolijs Naumčiks – International Journal of Reproduction, Contraception, Obstetrics and Gynecology

Human respiratory microbiome

Conference abstract: Profiling of lung microbial communities in lung cancer and chronic obstructive pulmonary disease patients – Yanhong Liu – Cancer Research

Human oral microbiome

Conference abstract: 16S rRNA saliva analysis unveils differences in the head and neck squamous cell carcinoma microbiome before and after surgical resection – Rafael E. Guerrero-Preston – Cancer Research

Human gut microbiome

Variable alterations of the microbiota, without metabolic or immunological change, following faecal microbiota transplantation in patients with chronic pouchitis – J. Landy – Scientific Reports

Review: Systematic Review of the Relation Between Intestinal Microbiota and Toll-Like Receptors in the Metabolic Syndrome: What Do We Know So Far? – José Pedro Portela-Cidade – GE Portuguese Journal of Gastroenterology

Review: Commensal Microbiome Promotes Resistance to Local and Systemic Infections – Nan Zhang – Chinese Medical Journal

Animal microbiome

High diversity of viable bacteria isolated from lymph nodes of slaughter pigs and its possible impacts for food safety – Evelyne Mann – Journal of Applied Microbiology

Geographic patterns in the bacterial microbiome of the glassy-winged sharpshooter, Homalodisca vitripennis (Hemiptera: Cicadellidae) – E. W. Welch – Symbiosis

Plant, root, and soil microbiome

Using direct amplification and next-generation sequencing technology to explore foliar endophyte communities in experimentally inoculated western white pines – Lorinda S. Bullington – Fungal Ecology

Maize lines with different nitrogen use efficiency select bacterial communities with different β-glucosidase-encoding genes and glucosidase activity in the rhizosphere – Shamina I. Pathan – Biology and Fertility of Soils

Fire severity shapes plant colonization effects on bacterial community structure, microbial biomass, and soil enzyme activity in secondary succession of a burned forest – Joseph E. Knelman – Soil Biology and Biochemistry

Diversity of hydrolases from hydrothermal vent sediments of the Levante Bay, Vulcano Island (Aeolian archipelago) identified by activity-based metagenomics and biochemical characterization of new esterases and an arabinopyranosidase – Antonio Placido – Applied Microbiology and Biotechnology

Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe – Jonathan W. Leff – PNAS

Soil Metagenomes from Different Pristine Environments of Northwest Argentina – Christina B. McCarthy – Genome Announcements

Relationships between the density and activity of microbial communities possessing arylsulfatase activity and soil sulfate dynamics during the decomposition of plant residues in soil – Séverine Piutti – European Journal of Soil Biology

Food microbiology

Microbial changes of natural milk cultures for mozzarella cheese during repeated propagation cycles – Angela Guidone – LWT – Food Science and Technology

No paper, just abstract, no pathogens appear to have been found: Culture-independent Pathogenic Bacterial Communities in Bottled Mineral Water – Hamdy A. Hassan – Renewable Energy & Sustainable Development

A diagnosis of the microbiological quality of dehydrated bee-pollen produced in Brazil – Adriane Alexandre Machado De-Melo – Letters in Applied Microbiology

Metagenomics and bioinformatics

HipMer: An Extreme-Scale De Novo Genome Assembler – Evangelos Georganas

Functional metagenomic discovery of bacterial effectors in the human microbiome and isolation of commendamide, a GPCR G2A/132 agonist – Louis J. Cohen – PNAS

Proteomics and metabolomics

The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity – Samuel H. Payne – Scientific Data

Monitoring microbial metabolites using an inductively coupled resonance circuit – Daniil Karnaushenko – Scientific Reports

Extremophiles

Biotechnological applications of extremophiles, extremozymes and extremolytes – Noura Raddadi – Applied Microbiology and Biotechnology

Microbes in the news

Mothers facing C-sections look to vaginal ‘seeding’ to boost their babies’ health – Aimee Molloy – The Guardian

Bacterial community in pregnant women linked to preterm birth, study finds – Erin Digitale – Stanford Medicine
Stanford preterm birth study counters Detroit findings – Karen Bouffard – The Detroit News
Microbe Mix May Play Role In Preterm Birth Risk – Rob Stein – NPR

Biologist investigates how gene-swapping bacteria evade antibiotics – University of Texas at Dallas – EurekAlert

Methane and Climate Change: Arctic Bacteria Might Eat Methane? – Nature World News

How beneficial bacteria protect intestinal cells – Quinn Eastman – Emory News Center

Researchers Identify Metaproteomic Differences between Obese, Non-Obese Individuals – Adam Bonislawski – Genomeweb

How does Cincinnati Children’s Hospital use the microbiome to study lupus? A look inside with Diana Taft – Megan McGrath – DNA Genotek

Science, publishing, and career

A Scientific Look at Bad Science – Bourree Lam – The Atlantic

Bik’s Picks

Photos: Ancient Flowering Plant May Have Lived with Dinosaurs – Live Science

First-Ever Salamander in Amber Found in Caribbean – Richard Farrell – Discovery

Nasa awards $200,000 grant to a research project aimed at turning astronaut poo into food – Independent

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August 17, 2015

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Gut microbiota composition is associated with stool consistency, sequencing the lung microbiome, and the importance of purses as fomites.

Events

Tuesday evening: The Microbiome: An Alien Organ Within the Human Body – OMSI Science Pub (18 August 2015), Portland, OR

Human respiratory microbiome

Integrating microbial and host transcriptomics to characterize asthma-associated microbial communities – Eduardo Castro-Nallar – BMC Medical Genomics

Editorial to the Sze article : Outside In: Sequencing the Lung Microbiome – Michael J. Cox – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Gut microbiota composition associated with stool consistency – E F Tigchelaar – Gut

Review: The role for gut permeability in the pathogenesis of type 1 diabetes – a solid or leaky concept? – Xia Li – Pediatric Diabetes

Animal microbiome

Buccal swabbing as a non-invasive method to determine bacterial, archaeal, and eukaryotic microbial community structure in the rumen – Sandra Kittelmann – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Olive Husk Compost Improves the Quality of Intensively Cultivated Agricultural Soils – María Teresa Moreno – Land Degradation & Development

Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities – Blaire Steven – Applied and Environmental Microbiology

Built environment microbiology

A study to investigate the importance of purses as fomites – Susheela D Biranjia-Hurdoyal – Advanced Biomedical Research

More microbiology

Review: Diagnostics and Discovery in Viral Central Nervous System Infections – Walter Ian Lipkin – Brain Pathology

(Meta)genomics

Getting the genome in shape: the formation of loops, domains and compartments – Britta AM Bouwman – Genome Biology

Microbes in the news

Bug-killing book pages clean murky drinking water: pages can be torn out to filter drinking water – Jonathan Webb – BBC

A geneticist says any new parent should ‘roll their child on floor of the New York subway’ — here’s why – Erin Brodwin – Business Insider

Having your rot on! In your compost pile you will find billions and billions of microbes with a voracious appetite for organic matter – Chuck Martin – Midland Daily News

Bacteria in flowers may boost honeybees’ healthy gut microbes: Honeybees were into probiotics way before they were cool, a new study suggests. – Beth Mole – Science News

The curious meeting of two partners: the squid–vibrio symbiosis – Tim Miyashiro – Society for General Microbiology

Horses: Heaves and Tracheal Microbiomes: Is There a Connection? – Erica Larson – The Horse

What’s on the menu? Bacteria – lots of them – Elisa Ung – North Jersey.com
“menus are usually the most bacteria-laden object on a restaurant table”

Oral bacteria: friends and foes of the mouth – Nikki Natividad – Rappler

TB Traces: The mummy museum in Vác, Hungary, has human remains that helped researchers learn more about the origins of tuberculosis in Europe – The Scientist

Bik’s Picks

The relationship between the season of birth and early-onset food allergies in children –
Kajiyo Tanaka – Pediatric Allergy and Immunology

NASA working on gecko-inspired, sticky-footed robot – Chuck Bednar – Red Orbit

Tour de Turtles: The Race to Save the Turtles and Maybe Humans as Well – Dave Randle – Huffington Post
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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 15, 2015

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Here is your Saturday edition of the Digest. Four papers today about Arctic water and soil microbes, oral bacteria in placentas, using hand microbiomes to identify human ethnicities, and machine learning classifiers give insights in bacterial vaginosis.

Pregnancy and birth microbiome

Oral bacteria in placental tissues: Increased molecular detection in pregnant periodontitis patients – Vanessa Blanc – Oral Diseases

Human skin microbiome

Hand bacteria as an identifier: a biometric evaluation – Amanda B. Holbert – Network Modeling Analysis in Health Informatics and Bioinformatics

Minireview: From Head to Toe: Mapping Fungi across Human Skin – Tim Sandle – EC Microbiology

Human respiratory microbiome

Impact of cigarette smoking on the middle meatus microbiome in health and chronic rhinosinusitis – Vijay R. Ramakrishnan – International Forum of Allergy & Rhinology

Human gut microbiome

Metagenomic Analysis of Crohn’s Disease Patients Identifies Changes in the Virome and Microbiome Related to Disease Status and Therapy, and Detects Potential Interactions and Biomarkers – Pérez-Brocal, Vicente – Inflammatory Bowel Diseases

Animal models

SIV-infection-driven changes of pattern recognition receptor expression in mesenteric lymph nodes and gut microbiota dysbiosis – Tiffany W. Glavan – Journal of Medical Primatology

Plant, root, and soil microbiome

Diazotrophic bacilli isolated from the sunflower rhizosphere and the potential of Bacillus mycoides B38V as biofertiliser – A. Ambrosini – Annals of Applied Biology

Relationships between Oak powdery mildew incidence and severity and commensal fungi – E. T. Topalidou – Forest Pathology

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity – Anastasia Bragina – Molecular Ecology

Warming reduces the cover and diversity of biocrust-forming mosses and lichens, and increases the physiological stress of soil microbial communities in a semi-arid Pinus halepensis plantation – Fernando T. Maestre – Frontiers in Microbiology

Microbial Mineral Colonization Across a Subsurface Redox Transition Zone – Brandon Converse – Frontiers in Microbiology

Mutabilis in mutabili: Spatiotemporal dynamics of a truffle colony in soil – Milan Gryndler – Soil Biology and Biochemistry

Water microbiome

Bacterioplankton community shifts associated with epipelagic and mesopelagic waters in the Southern Ocean – Zheng Yu – Scientific Reports

Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period – Anne Poste – Frontiers in Microbiology

Extremophile microbiome: Arctic edition

Microbial activity is not always limited by nitrogen in Arctic tundra soils – Caroline Melle – Soil Biology and Biochemistry

Arctic soil microbial diversity in a changing world – Aimeric Blaud – Research in Microbiology

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

Diversity of planktonic microorganisms in the Arctic Ocean – Carlos Pedrós-Alió – Progress in Oceanography

Waste treatment microbiology

Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge – Ariane Bize – Proteomics

Bioinformatics

Machine learning classifiers provide insight into the relationship between microbial communities and bacterial vaginosis – Daniel Beck – BioData Mining

AmpliSAS: a web server for multilocus genotyping using next-generation amplicon sequencing data – Alvaro Sebastian – Molecular Ecology Resources

Science, publishing, and career

My alma mater, Utrecht University was again voted as the best Dutch university! Academic Ranking of World Universities 2015 – Shanghai Ranking

Microbes in the news

The Microbial Discovery Box: a hands-on activity for science teachers – ASM

Young scientists dreaming big: internship presentation competitions – Uganda Virus Research Institute

Infectious Diseases Like It Hot: How Climate Change Helps Cholera and Salmonella Outbreaks – Marlene Cimons – Think Progress

Before an Animal Disease Becomes a Human Epidemic – Cari Romm – The Atlantic

The dangers of eating snakes: Gauteng pastor encouraged his congregation to eat hair and snakes.

Bik’s Picks

Air Problem Is Worse Than You Think – James Fallows – The Atlantic

Georgia court weighs destiny of 18 captured beluga whales – Rich McKay – Reuters

Los Angeles Throws 96M Balls At California’s Drought Problem – Science Daily

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