Category Archives: Human oral

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 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 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 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 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 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 6, 2015

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Obesity in Korean adolescents, banana rhizosphere, rare taxa and Deepwater Horizon spill, leaking septic tanks, and visualization of ‘omics data.

Events

BioMicroWorld 2015: International Conference on Environmental, Industrial and Applied Microbiology, 28-30 October 2015, Barcelona, Spain – Has a workshop called: “Modelling bacterial dynamics using the R software”

Human oral and gut microbiome

Oral and faecal microbiota in volunteers with hypertension in a double blind, randomised placebo controlled trial with probiotics and fermented bilberries – Jie Xu – Journal of Functional Foods

Obesity Alters the Microbial Community Profile in Korean Adolescents – Hae-Jin Hu – PLOS ONE

Microbiome models

Rescue of Fructose-Induced Metabolic Syndrome by Antibiotics or Faecal Transplantation in a Rat Model of Obesity – Blanda Di Luccia – PLOS ONE

Plants, roots, and soil microbiome

Manipulating the banana rhizosphere microbiome for biological control of Panama disease – Chao Xue – Scientific Reports

Review: Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity – Barbara Reinhold-Hurek – Annual Review of Phytopathology

Effect of Agricultural Amendments on Cajanus cajan (Pigeon Pea) and Its Rhizospheric Microbial Communities – A Comparison between Chemical Fertilizers and Bioinoculants – Rashi Gupta – PLOS ONE

Effect of genetically modified rice producing resveratrol on the soil microbial communities – Soo-In Sohn – Journal of the Korean Society for Applied Biological Chemistry

Water microbiome

Diverse, rare microbial taxa responded to the Deepwater Horizon deep-sea hydrocarbon plume – Sara Kleindienst – The ISME Journal

Linking fecal bacteria in rivers to landscape, geochemical, and hydrologic factors and sources at the basin scale – Marc P. Verhougstraete – PNAS

Toolbox approaches using molecular markers and 16S rDNA amplicon datasets for the identification of fecal pollution in surface water – W. Ahmed – Applied and Environmental Microbiology

Bioinformatics

Anvi’o: An advanced analysis and visualization platform for ‘omics data – A. Murat Eren – Peer J

InteMAP: Integrated metagenomic assembly pipeline for NGS short reads – Binbin Lai – BMC Bioinformatics

MiRKAT peeks at associations between the microbiome and disease – —JM Kocarnik – Fred Hutch

Fungi and microbiomes

Noisy neighbourhoods: quorum sensing in fungal polymicrobial infections – Emily F. Dixon – Cellular Microbiology

Metabarcoding analysis of home composts reveals distinctive fungal communities with a high number of unassigned sequences – Adrian Langarica-Fuentes – Microbiology

More microbes

Review: Next-generation sequencing for pathogen detection and identification – Kenneth G. Frey – Methods in Microbiology

Microbes in the news

University of Missouri hosts open house at DNA sequencing center – Megan Favignano – Columbia Tribune

Detective work traces bacteria in Michigan rivers back to leaky septic tanks – Rebecca Williams – Michigan Radio

Bacteria that may cause spotty liver disease in chickens identified – Farmers Weekly

Bik’s Picks

World’s first ant map launched in Hong Kong:geographic locations of nearly 15,000 types of ant – Business Insider

Seeds That Defied Romans, Pirates, and Nazis – Robert Krulwich – National Geographic

The dark side of the moon sails across Earth in new NASA video – Deborah Netburn – Los Angeles Times

 

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