Category Archives: Waste and pollution

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 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 24, 2015

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Microbiome of death

Soil fungal community shift evaluation as a potential cadaver decomposition indicator –
Monica Chimutsa – Forensic Science International

Pregnancy and birth

Master Thesis – The Association of Necrotizing Enterocolitis with Integrons and Antibiotic Resistance Genes in the Gut Microbiota of Preterm Infants – Eva Lena F. Estensmo – Norwegian University of Life Sciences

Human respiratory microbiome

Regional Isolation Drives Bacterial Diversification within Cystic Fibrosis Lungs – Peter Jorth – Cell Host & Microbe

Quantitative analysis of pathogens in the lower respiratory tract of patients with chronic obstructive pulmonary disease – Huaying Wang – BMC Pulmonary Medicine

Animal microbiome

Evidence-based recommendations on storing and handling specimens for analyses of insect microbiota – Tobin J Hammer – Peer J

Path analyses of cross-sectional and longitudinal data suggest that variability in natural communities of blood-associated parasites is derived from host characteristics and not interspecific interactions – Carmit Cohen – Parasites & Vectors

Plant, root, and soil microbiome

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest – Jing Cong – BMC Microbiology

Disentangling the ‘brown world’ faecal-detritus interaction web: dung beetle effects on soil microbial properties – Eleanor M. Slade – Oikos

Taxon-specific responses of soil microbial communities to different soil priming effects induced by addition of plant residues and their biochars – Peng Su – Journal of Soils and Sediments

Research Highlight: Root recruiting – Mirella Bucci – Nature Chemical Biology

Water microbiome

Habitat and water quality variables as predictors of community composition in an Indonesian coral reef: a multi-taxon study in the Spermonde Archipelago – Ana Rita Moura Polónia – Science of the Total Environment

Waste water microbiology

Persistence of Ebola Virus in Sterilized Wastewater – Kyle Bibby – Environmental Science & Technology Letters

Metagenomics and bioinformatics

MetaObtainer: A Tool for Obtaining Specified Species from Metagenomic Reads of Next-generation Sequencing – Weihua Pan – Interdisciplinary Sciences: Computational Life Sciences

Minimum Information about a Biosynthetic Gene cluster – Marnix H Medema – Nature Chemical Biology

Viruses

A protein domain-based view of the virosphere-host relationship – Aare Abroi – Biochimie

Microbes in the news

Add Lots of Microbes to ‘Me, Myself, and I’ – David Salisbury – Futurity

The Microbiome Is Science’s Hot New Kid – Anand Veeravagu and Tessa Anderman – The Daily Beast

Science Briefs: Topography of spinach leaf shelters bacteria – John Bordsen – Charlotte Observer

Inside N.C. Science: Bugs – and mates – attracted by body odor – Sarah Council – Charlotte Observer

Universal flu vaccine comes closer, scientists say – Michelle Roberts – BBC News

Science, publishing, and career

Here’s what two college doctors say freshman need to know – LaTasha Seliby and Ranit Mishori – Washington Post

Women, minorities still underrepresented in medical specialties – Megan Brooks – Reuters

Bik’s Picks

Japanese Spacecraft Delivers Mice, Booze and More to ISS – Sarah Lewin – NBC News

Biologists Have Spotted the First Wolf Pack in California in 100 Years – Marissa Fessenden – Smithsonian

Get the Bunsen burner out: It’s time to concoct dinner – Nancy Szokan – Washington Post

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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 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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August 12, 2015

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

General microbiome

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

Pregnancy and birth microbiome

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

Human gut microbiome

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

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

Animal and other models

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

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

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

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

Water microbiome

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

Waste and water treatment microbiology

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

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

More microbes

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

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

Microbes in the news

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

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

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

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

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

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

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

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

Science, publishing, and career

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

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

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

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

Bik’s Picks

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

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

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

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August 11, 2015

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Several reviews on human gut microbiome, two papers on coral microbiome, gut microbiota of wild mice, ancient sea microbes found in gold mine stalactites, and an update on the tree of life.

Microbiome of Death

Not a microbiota paper, but cannot leave out: A Longitudinal Study on Human Outdoor Decomposition in Central Texas – Joanna K. Suckling – Journal of Forensic Sciences

Human gut microbiome

Anti-tumour Necrosis Factor Treatment with Adalimumab Induces Changes in the Microbiota of Crohn’s Disease – David Busquets – Journal of Crohn’s and Colitis

Reduced Levels of D-dimer and Changes in Gut Microbiota Composition after Probiotic Intervention in HIV-infected Individuals on Stable ART – Birgitte Stiksrud – Journal of Acquired Immune Deficiency Syndromes

The human gut microbiome as a transporter of antibiotic resistance genes between continents – Johan Bengtsson-Palme – Antimicrobial Agents and Chemotherapy

Review: The gut microbiota in human energy homeostasis and obesity – Michael Rosenbaum – Trends in Endocrinology & Metabolism

Review: Understanding probiotics’ role in allergic children: the clue of gut microbiota profiling – Pamela Vernocchi – Current Opinion in Allergy and Clinical Immunology

Editorial: The Role of Bacteria in Necrotizing Enterocolitis: Understanding the Forest for the Trees – McElroy S.J – Neonatology

Review: Implications of microbiota and bile acid in liver injury and regeneration – Hui-Xin Liu – Journal of Hepatology

Animal and bioreactor models

Metagenomic Analysis of Antibiotic Resistance Genes in Dairy Cow Feces following Therapeutic Administration of Third Generation Cephalosporin – Lindsey Chambers – PLOS ONE

Increased Butyrate Production During Long-Term Fermentation of In Vitro-Digested High Amylose Cornstarch Residues with Human Feces – Li Li – Journal of Food Science

Bacterial diversity in bovine rumen by metagenomic 16S rDNA sequencing and scanning electron microscopy – Raphael Barbetta de Jesus – Acta Scientiarum

Animal microbiome

The Gut Microbiota of Wild Mice – Laura Weldon – PLOS ONE

Necrotizing Enterocolitis in Preterm Pigs Is Associated with Increased Density of Intestinal Mucosa-Associated Bacteria Including Clostridium perfringens – Støy A.C.F. – Neonatology

Cecal drop reflects the chickens’ cecal microbiome, fecal drop does not – J. Pauwels – Journal of Microbiological Methods

Evidence for host specificity among dominant bacterial symbionts in temperate gorgonian corals – Marie La Rivière – Coral Reefs

Identification of Candidate Coral Pathogens on White Band Disease-Infected Staghorn Coral – Sarah A. Gignoux-Wolfsohn – PLOS ONE

Bacteria detected in the honeybee parasitic mite Varroa destructor collected from beehive winter debris – J. Hubert – Journal of Applied Microbiology

Plant, root, and soil microbiome

Remediation of diesel-contaminated soil using in situ chemical oxidation (ISCO) and the effects of common oxidants on the indigenous microbial community: a comparison study – Ku-Fan Chen – Journal of Applied Microbiology

Rhizosphere bacterial communities of dominant steppe plants shift in response to a gradient of simulated nitrogen deposition – An Yang – Frontiers in Microbiology

Diversity and Distribution of Archaea in the Mangrove Sediment of Sundarbans – Anish Bhattacharyya – Archaea

Seasonal effect and anthropogenic impact on the composition of the active bacterial community in Mediterranean orchard soil – Sammy Frenk – FEMS Microbial Ecology

Effects of biochar on copper immobilization and soil microbial communities in a metal-contaminated soil – Sebastián Meier – Journal of Soils and Sediments

Factors associated with the diversification of the microbial communities within different natural and artificial saline environments – Shilong He – Ecological Engineering

Review: Direct and indirect effects of climate change on soil microbial and soil microbial-plant interactions: What lies ahead? – Aimée T. Classen – Ecosphere

Water microbiome

Deep subsurface mine stalactites trap endemic fissure fluid Archaea, Bacteria, and Nematoda possibly originating from ancient seas – Gaëtan Borgonie – Frontiers in Microbiology

Drivers of the dynamics of diazotrophs and denitrifiers in North Sea bottom waters and sediments – Haoxin Fan – Frontiers in Microbiology

Waste treatment microbiology

Denitrifying capability and community dynamics of glycogen accumulating organisms during sludge granulation in an anaerobic-aerobic sequencing batch reactor – Zhang Bin – Scientific Reports

Proteomics

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data – Laurence Yang – PNAS

Colonic metaproteomic signatures of active bacteria and the host in obesity – Carolin A. Kolmeder – Proteomics

More microbes

The universal tree of life: an update – Patrick Forterre – Frontiers in Microbiology

How Do Microbial Populations and Communities Function as Model Systems? – Maureen O’Malley – The Quarterly Review of Biology

Impact of space flight on bacterial virulence and antibiotic susceptibility – Peter William Taylor – Infection and Drug Resistance

Microbes in the news

Look Up! There’s an Invisible Zombie Highway Right Above You – Robert Krulwich – National Geographic

uBiome Invites Health Care Providers to Join New Clinical Microbiome Consortium – Global News Wire

Our microbiome: Separating hype from health – Nicholas Staropoli – Genetic Literacy Project

Poop Transplants And Microbiome Makeovers: How We’ll Engineer Our Bacteria To Feel Better – Jessica Leber – FastCoExist

Researchers Offer New Insights Into the Pulmonary Microbiota of Cystic Fibrosis Patients – Patricia Silva – Cystic Fibrosis News Today

Conflict and Co-operation in Bacterial Communities – MicrobePost

Can Your Body’s Bacteria Cause Cancer? – Charis Eng – Cleveland Clinic

British Ministry of Defense released potentially lethal bacteria on London Tube (in 1963), chemically experimented on soldiers – Russell Boyce – RT

Engineered Bacteria Send A Signal When Water Gets Polluted – Tracy Staedter – Discovery

JGI to Grant $1.2 Million to Genomic Technology Projects – Genome Web

Science, publishing, and career

Science: The Story of Me – Morgan Pak – Huffington Post

4 Ways to Help Everyone Find Their Inner Scientist – Imogen Coe – Huffington Post

Tech Women in India’s Startup Boom Reach Out – Gagandeep Kaur – WomensEnews

Bik’s Picks

Magnetosensitive neurons mediate geomagnetic orientation in Caenorhabditis elegans – Andrés Vidal-Gadea – eLIFE

Here’s why coffee makes you poop – Rachel Feltman – Washington Post

Why You’re More Likely To Be Killed By a Bee Than a Bear: Our fear of bear attacks is far greater than the actual risk of being mauled or killed, experts say. – Carrie Arnold – National Geographic

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August 10, 2015

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Ammonia oxidizing bacteria in urban soil, respiratory tract microbiota in Cystic Fibrosis, and colonization of sewer systems.

Human respiratory microbiome

Insights into the respiratory tract microbiota of patients with cystic fibrosis during early Pseudomonas aeruginosa colonization – Marlène Keravec – Springer Plus

Animal microbiome

Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes – Analice C. Azevedo – Applied and Environmental Microbiology

Interactions between co-occurring lactic acid bacteria in the honey bee hive – Z.P. Rokop – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Combined Flux Chamber and Genomics Approach Links Nitrous Acid Emissions to Ammonia Oxidizing Bacteria and Archaea in Urban and Agricultural Soil – Nicole K. Scharko – Environmental Science & Technology

Microhabitat heterogeneity across leaves and flower organs promotes bacterial diversity – Robert R. Junker – FEMS Microbiology Ecology

Influence of physicochemical and nutritional factors on bacterial diversity in mangrove sediments along the southwest coast of Tamilnadu, India – S. Prakash – Environmental Monitoring and Assessment

Isolation and Screening of Rhizosphere Bacteria from Grasses in East Kavango Region of Namibia for Plant Growth Promoting Characteristics – D. H. Haiyambo – Current Microbiology

Long-term oil contamination causes similar changes in microbial communities of two distinct soils – Jingqiu Liao – Applied Microbiology and Biotechnology

Waste treatment microbiology

Profile and fate of bacterial pathogens in sewage treatment plants revealed by high-throughput metagenomic approach – Bing Li – Environmental Science & Technology

Changes of microbial biofilm communities during colonization of sewer systems – O Auguet – Applied and Environmental Microbiology

Impacts of Long-term Irrigation of Domestic Treated Wastewater on Soil Biogeochemistry and Bacterial Community Structure – Denis Wafula – Applied and Environmental Microbiology

Metagenomics

Genomes analysis and bacteria identification: The use of overlapping genes as molecular markers – Elena Perrin – Journal of Microbiological Methods

Review: From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems – Daniel R. Garza – Cellular and Molecular Life Sciences

Microbes in the news

I’ll Take My Latte with a Shot of Bacteria
 – Carrie Arnold – The Daily Beast

UO architect and microbiologist explore how home weatherization affects beneficial bacteria – Diane Dietz – The Register-Guard

Are Microbes Stealing Your Mind? Could bacteria hold the answer to an Alzheimer’s cure? Some researchers say yes. – David Ewing Duncan – The Daily Beast

This one made me laugh: No bacteria found in popular sandwiches: Taiwan FDA. “The FDA said the tests only showed Staphylococcus arouse” (sic)

Very rhetoric piece with lots of adjectives, some science, and lots of nonsense:
How The Microbiome Destroyed the Ego, Vaccine Policy, and Patriarchy – Sayer Ji – GreenMedInfo

Bik’s Picks

Massive ‘Communal’ Spider Webs Emerge in Dallas Suburb – Richard Farrell – Discovery

Coca-Cola is funding obesity research with a biased message, nutrition experts say – Ariana Eunjung Cha – Washington Post

Here’s why goats have those freaky eyes – Rachel Feltman – Washington Post
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