Category Archives: More Microbes

October 6, 2015

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Human gut microbiome

Intersections between Microbiome and Heart Failure: Revisiting the Gut Hypothesis –
Yuji Nagatomo – Journal of Cardiac Failure

Phenolic compounds from red wine and coffee are associated with specific intestinal microorganisms in allergic subjects – Adriana Cuervo – Food and Function

Review: The Human Microbiota: Composition, Functions, and Therapeutic Potential – Rick Conrad, Alexander V. Vlassov – Medical Science Review

Models of microbiome research

Inflammation-associated alterations to the intestinal microbiota reduce colonization resistance against non-typhoidal Salmonella during concurrent malaria parasite infection – Jason P. Mooney – Scientific Reports

Protocols for the Use of Gut Models to Study the Potential Contribution of the Gut Microbiota to Human Nutrition Through the Production of Short-Chain Fatty Acids –
Andrew J McBain – Springer Protocols Handbooks

Salami? Cecum microbial communities from steers differing in feed efficiency – P. R. Myer – Journal of Animal Science

Animal microbiome

Dholes are a species of wild dog: First report on the bacterial diversity in the distal gut of dholes (Cuon alpinus) by using 16S rRNA gene sequences analysis – Lei Chen – Journal of Applied Genetics

Plant, root, and soil microbiome

Diversity of fungi associated with plants growing in geothermal ecosystems and evaluation of their capacities to enhance thermotolerance of host plants – Wen-Na Zhou – Journal of Plant Interactions

Forage crops alter soil bacterial and fungal communities in an apple orchard – Sijun Qin – Acta Agriculturae Scandinavica, Section B — Soil & Plant Science

Bacterial communities estimated by pyrosequencing in the soils of chinampa, a traditional sustainable agro-ecosystem in Mexico – Salvador Embarcadero-Jiménez – Journal of Soils and Sediments

Water microbiome

Bacterial diversity and community composition from seasurface to subseafloor – Emily A Walsh – The ISME Journal

Modelling the effects of hydrodynamic regimes on microbial communities within fluvial biofilms: combining deterministic and stochastic processes – Yi Li – Environmental Science & Technology

A new tool for long-term studies of POM-bacteria interactions: overcoming the century-old Bottle Effect – Danny Ionescu – Scientific Reports

Book chapter: Protistan Diversity in Environmental Molecular Surveys – Ramon Massana – Marine Protists

Book chapter: Diversity of Microbial Eukaryotes in Deep Sea Chemosynthetic Ecosystems Illuminated by Molecular Techniques – Kiyotaka Takishita – Marine Protists

Extremophile microbiome

Metagenomic and metatranscriptomic analyses of Lake Vostok accretion ice – Yury M. Shtarkman – Bowling Green State University

Metabolic networks, proteomics

Gastrointestinal symptoms and altered intestinal permeability induced by combat-training are associated with distinct metabotypic changes – Lee Cheng Phua – Journal of Proteome Research

Review: Roles of Indole as an Interspecies and Interkingdom Signaling Molecule – Jin-Hyung Lee – Trends in Microbiology

Bioinformatics and metagenomics

Comparison of three clustering approaches for detecting novel environmental microbial diversity – Dominik Forster – PeerJ Preprints

MG-RAST, a Metagenomics Service for the Analysis of Microbial Community Structure and Function – Elizabeth M. Glass, Folker Meyer – Springer Protocols Handbook

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering – Oscar Franzén – Microbiome

Techniques

An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms – Hooman Derakhshani – Journal of Basic Microbiology

More microbiology

This paper contains large amounts of plagiarism and confusing images, but here it is: Microbial Forensics in Legal Medicine – Pankaj Shrivastava – SAS Journal of Medicine

Microbes in the news

Georgia State Researcher Gets $1.35 Million to Study Effects of Common Food Additive on Body – Georgia State University
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September 28, 2015

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Pregnancy and birth

Eczema susceptibility and composition of faecal microbiota at four weeks of age: A pilot study in Chinese infants – M.F. Tang – British Journal of Dermatology

Human skin microbiome

Prevalence and antibiotic susceptibility of bacteria from acute and chronic wounds in Malaysian subjects – Shin Yee Wong – The Journal of Infection in Developing Countries

Human respiratory microbiome

Induced sputum in young healthy children with cystic fibrosis – Julian Forton – Paediatric Respiratory Reviews

Human urinary tract microbiome

Assessment of the Lower Urinary Tract Microbiota during Symptom Flare in Women with Urologic Chronic Pelvic Pain Syndrome: A MAPP Network Study – J. Curtis Nickel – The Journal of Urology

Human gut microbiome

Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer – Jun Yu – Gut

Animal microbiome

Abundance of ruminal bacteria, epithelial gene expression, and systemic biomarkers of metabolism and inflammation are altered during the peripartal period in dairy cows – A. Minuti – Journal of Dairy Science

Plant, root, and soil microbiome

Bacterial endophyte communities in the foliage of coast redwood and giant sequoia – Alyssa A. Carrell and Anna C. Frank – Frontiers in Microbiology

Root isolations of Metarhizium spp. from crops reflect diversity in the soil and indicate no plant specificity – Bernhardt M. Steinwender – Journal of Invertebrate Pathology

DGGE: Biogas digestates affect crop P uptake and soil microbial community composition –
Sebastian Hupfauf – Science of The Total Environment

Water microbiome

Meta-omic signatures of microbial metal and nitrogen cycling in marine oxygen minimum zones – Jennifer B. Glass – Frontiers in Microbiology

Extremophile microbiome

Snow and ice ecosystems: not so extreme – Lorrie Maccario – Research in Microbiology

Metagenomics and bioinformatics

PanFP: pangenome-based functional profiles for microbial communities – Se-Ran Jun – BMC Research Notes

More microbes

The Out-of-the-Delta Hypothesis: dense human populations in low-lying river deltas served as agents for the evolution of a deadly pathogen – Yan Boucher – Frontiers in Microbiology

Techniques

Blocking primers reduce co-amplification of plant DNA when studying bacterial endophyte communities – Brett E. Arenz – Journal of Microbiological Methods

Microbes in the news

Infections in childhood could provide clues to disease development in later life – European Lung Foundation – EurekAlert

Harnessing The Hordes In The Microbiome: As researchers learn more about the connection between our bacteria and our health, companies are trying to develop therapies that exploit it – Lisa M. Jarvis – Chemical and Engineering News

Dried plums cuts risk of colon cancer, research reveals – Karla Tecson – International Business Times

Root microbiome engineering improves plant growth – EurekAlert

What could possibly go wrong? NASA Is Sending Bacteria to the Edge of Space to See if They Can Hitchhike to Mars – Maddie Stone – Gizmodo

Move over, Barry Marshall: 3.5-Million-Year Old Bacteria: Found To Boost Longevity In Lab Tests, Russian Scientist Injects Self – Aditi Simlai Tiwari – HNGN

Science, publishing, and career

High time for a common plagiarism detection system – Ivan Jarić – Scientometrics

It’s Peer Review Week: 28 Sep – 2 Oct 2015
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September 21, 2015

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Microbiome Digest is back!

Today’s digest features nasal microbiomes of infants, oral microbiome of denture wearers, skin microbiome composition and outcome of infection, Atacama desert soil microbiome, and a comprehensive tree of life.

General microbiome

Viewpoint: The Human Microbiome and the Future Practice of Medicine – David A. Relman – JAMA

Review: Understanding Microbiome Data: A Primer for Clinicians – Seksik P. – Digestive Diseases

Pregnancy and birth microbiome

Minimally Invasive Sampling Method Identifies Differences in Taxonomic Richness of Nasal Microbiomes in Young Infants Associated with Mode of Delivery – Meghan H. Shilts – Host Microbe Interactions

Review: Microbiome and pediatric atopic dermatitis – Claire E. Powers – The Journal of Dermatology

Editorial: Metaproteomic analysis adds a functional glimpse into host-microbe succession in an infant’s GI – Joshua E. Elias – Proteomics

Human oral microbiome

The Oral Microbiome of Denture Wearers Is Influenced by Levels of Natural Dentition – Lindsay E. O’Donnell – PLOS ONE

Forensic Identification in Teeth with Caries – Esther Alia-García – Forensic Science International

Review: Oral Microbiome Metabolism: From “Who Are They?” to “What Are They Doing?” – N. Takahashi – Journal of Dental Research

Review: Polymicrobial Candida biofilms: friends and foe in the oral cavity – Lindsay E. O’Donnell – FEMS Yeast Research
Review: Defining periodontal health – Angelo Mariotti and Arthur F Hefti – BMC Oral Health

Review: Can oral infection be a risk factor for Alzheimer’s disease? – Ingar Olsen and Sim K. Singhrao – Journal of Oral Microbiology

Review: The commensal microbiota and the development of human disease – an introduction – Philip D. Marsh – Journal of Oral Microbiology

Human skin microbiome

The Human Skin Microbiome Associates with the Outcome of and Is Influenced by Bacterial Infection – Julia J. van Rensburg – mBio

Review: Turning the inside out: The microbiology of atopic dermatitis – Harald Brüssow – Environmental Microbiology

Review: Microbiome and pediatric atopic dermatitis – Claire E. Powers – The Journal of Dermatology

Human gut microbiome

Decompensated cirrhosis and microbiome interpretation – Jasmohan S. Bajaj – Nature

The role of whole-grain barley on human fecal microbiota and metabolome – Maria De Angelis – Applied and Environmental Microbiology

Experimental hookworm infection and escalating gluten challenges are associated with increased microbial richness in celiac subjects – Paul Giacomin – Scientific Reports

Intestinal microbiota and anastomotic leakage of stapled colorectal anastomoses: a pilot study – Jasper B. van Praagh – Surgical Endoscopy

Dysbiosis in the Gut Microbiota of Patients with Multiple Sclerosis, with a Striking Depletion of Species Belonging to Clostridia XIVa and IV Clusters – Sachiko Miyake – PLOS ONE

Identification of key taxa that favor intestinal colonization of Clostridium difficile in an adult Chinese population – Silan Gu- Microbes and Infection

Long Term Development of Gut Microbiota Composition in Atopic Children: Impact of Probiotics – N. B. M. M. Rutten – PLOS ONE

Review: Does the buck stop with the bugs?: an overview of microbial dysbiosis in rheumatoid arthritis – Pulukool Sandhya – International Journal of Rheumatic Diseases

Review: Potential role of gut microbiota and tissue barriers in Parkinson’s disease and amyotrophic lateral sclerosis – Xin Fang – International Journal of Neuroscience

Editorial: Did you know that your cravings might be microbes controlling your mind? –
A. Zakrisson – Acta Physiologica

Human reproductive tract microbiome

Vaginal microbiome and metabolome highlight specific signatures of bacterial vaginosis –
B. Vitali – European Journal of Clinical Microbiology & Infectious Diseases

Plant, root, and soil microbiome

In situ metabolism in halite endolithic microbial communities of the hyperarid Atacama Desert – Alfonso F. Davila – Frontiers in Microbiology

Pervasive Effects of Wildfire on Foliar Endophyte Communities in Montane Forest Trees –
Yu-Ling Huang – Plant Microbe Interactions

Interrelated effects of mycorrhiza and free-living nitrogen fixers cascade up to aboveground herbivores – Botir Khaitov – Ecology and Evolution

Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences – M. Jeanbille – Soil Microbiology

Composition of fungal soil communities varies with plant abundance and geographic origin – Vanessa Reininger – AoB Plants

Analysis of a Pool of Small Plasmids from Soil Heterotrophic Cultivable Bacterial Communities – Maria Cristiana Papaleo – The Open Microbiology Journal

Water microbiome

Influence of streambed substratum composition on stream microbial communities exposed to the fungicide tebuconazole – Florence Donnadieu – Freshwater Biology

Built environment microbiome

Microbial Density on Electronic Devices – Sulan Kith – Int.J.Curr.Microbiol.App.Sci

Food microbiology

The microbiota of high-moisture mozzarella cheese produced with different acidification methods – Angela Guidone – International Journal of Food Microbiology

Review: Metagenomic insights into the dynamics of microbial communities in food –
Gilles Kergourlay – International Journal of Food Microbiology

Bioinformatics and metagenomics

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data – Jeremy A. Frank – BioRxiv

More microbes

Synthesis of phylogeny and taxonomy into a comprehensive tree of life – Cody E. Hinchliff – PNAS

Single cell activity reveals direct electron transfer in methanotrophic consortia –
Shawn E. McGlynn – Nature

Linking microbial community structure and microbial processes: an empirical and conceptual overview – Raven L. Bier – FEMS Microbial Ecology

Microbes in the news

Russian scientists make progress on secret of eternal life: Living bacteria found in permafrost – ‘3.5 million years old’ – is ‘scientific sensation’ which allows ‘mice grannies’ to reproduce. – The Siberian Times

Bacteria light up Rome’s Colosseum in ‘message of peace’ – Isla Binnie – Reuters

Son takes up fight against bacteria that took father’s leg – Daphne Chen – Washington Times

The frightening spread of antibiotic resistance around the world, visualized- Amy X. Wang – Quartz

Electron transport between species discovered in deep-sea research – Marilyn Malara – UPI

Feeding the world with microbacterial agriculture – Wendy Zukerman – The Saturday Paper
The bacteria-fighting super element that’s making a comeback in hospitals: copper – Lena H. Sun – Washington Post

St. Petersburg home brewer pushes the limits with wild bacteria beers – Michelle Stark – Tampa Bay

Scientists Create 1st ‘Tree of Life’ for Around 2.3 mn Species – TV Newsroom

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September 11, 2015

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Gates Foundation grant proposals, microbiome of the Amazon river. It’s too early here in Europe to get the new Pubmed  and other alerts, so a very short Digest today.

Call for proposals

The Bill and Melinda Gates Foundation put up several calls for grant proposals:

  • Addressing Newborn and Infant Gut Health Through Bacteriophage-Mediated Microbiome Engineering
  • Novel Approaches to Characterizing and Tracking the Global Burden of Antimicrobial Resistance

Rethinking heritability of the microbiome – Edward J. van Opstal, Seth R. Bordenstein – Science

Human gut microbiome

Review: Ecology and Evolution of the Human Microbiota: Fire, Farming and Antibiotics
Michael R. Gillings – Genes

Water microbiome

Metagenomic and metatranscriptomic inventories of the lower Amazon River, May 2011 – Brandon M. Satinsky – Microbiome

Microbes in the news

A World First: Pherecydes Pharma Launches Multicenter Clinical Study Of Phage Therapy In Serious Burn Victims – Biospace

New research finds balance between ‘good’ and ‘bad’ bacteria in humans altered – Medical Xpress

Your stomach bacteria determines which diet is best for weight reduction – HealthCanal

Latest military lab concerns involve plague bacteria, deadly viruses – Tom Vanden Brook and Alison Young – USA Today

Bacteria Bandage: Prototype Made Of Innovative Nanofibers Cleans Wounds, Prevents Infection – Susan Scutti – Medical Daily

A Novel Device That Can Sniff Out Bacteria in Drinking Water – NDTV

Science, publishing, and career

Nice to know you: “But then we tried an often overlooked strategy: Share an office!”
Malou Henriksen-Lacey, Juan J. Giner-Casares – Science

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September 5, 2015

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Events

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

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

General microbiome

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

Pregnancy and birth microbiome

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

Human oral microbiome

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

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

Human gut microbiome

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

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

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

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

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

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

Human respiratory microbiome (see also gut microbiome above)

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

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

Human other sites

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

Microbiome models

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

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

Animal microbiome

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

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

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

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

Plant, root, and soil microbiome

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

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

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

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

Water microbiome

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

Built environment microbiome

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

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

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

Food microbiology

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

Bioinformatics

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

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

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

More Microbiology

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

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

Microbes in the news

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

Science, publishing and career

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

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August 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 17, 2015

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

Events

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

Human respiratory microbiome

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

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

Human gut microbiome

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

Built environment microbiology

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

More microbiology

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

(Meta)genomics

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

Microbes in the news

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

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

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

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

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

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

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

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

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

Bik’s Picks

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

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

Tour de Turtles: The Race to Save the Turtles and Maybe Humans as Well – Dave Randle – Huffington Post
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August 14, 2015

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Two papers on detection of bacteria in blood, vaginal microbiome, a discussion on eukaryotes in the human gut, and fungal communities’ resistance and resilience to wild fires. And some extra non-microbial Bik’s Picks for the weekend!

Human blood / infection microbiome

Bacterial Landscape of Bloodstream Infections in Neutropenic Patients via High Throughput Sequencing – Peter Gyarmati – PLOS ONE

16S rRNA Gene Sequence-Based Identification of Bacteria in Automatically Incubated Blood Culture Materials from Tropical Sub-Saharan Africa – Hagen Frickmann – PLOS ONE

Human vaginal microbiome

A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types – Arianne Y. K. Albert – PLOS ONE

Human gut microbiome

Are Human Intestinal Eukaryotes Beneficial or Commensals? – Julius Lukeš – PLOS Pathogens

Review: Role of the normal gut microbiota – Sai Manasa Jandhyala – World Journal of Gastroenterology

Review: Paleolithic nutrition for metabolic syndrome: systematic review and meta-analysis – Eric W Manheimer – The American Journal of Clinical Nutrition

Animal models

In Mice: Autophagy Protects against Colitis by the Maintenance of Normal Gut Microflora and Secretion of Mucus – Koichiro Tsuboi – Journal of Biological Chemistry

Plant, root, and soil microbiome

Arbuscular mycorrhizal fungal communities show low resistance and high resilience to wildfire disturbance – Xingjia Xiang – Plant and Soil

From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization – Xiaofang Li – Scientific Reports

Water microbiome

A Dissolved Oxygen Threshold for Shifts in Bacterial Community Structure in a Seasonally Hypoxic Estuary – Rachel L. Spietz – PLOS ONE

Techniques

Collection media and delayed freezing effects on microbial composition of human stool – Roberto Flores – Microbiome

Bioinformatics

Sorting out viral dark matter – Denise Waldron – Nature Reviews Microbiology

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction – Jonas Paulsen – PLOS Computational Biology

Other microbiology

Mycobacterium tuberculosis: Genome watch: Looking at Beijing’s skyline – Dorota Jamrozy & Teemu Kallonen – Nature Reviews Microbiology

Microbes in the news

Feeding My Curiosity – And My Microbes – Alanna Collen – uBiome

Crohn’s and Colitis video featuring Laboratory of Will DePaolo

Bik’s Picks – some extra for you for the weekend!

We’ve Used Up Our Annual Supply of Earth’s Resources—And It’s Only August – Maddie Stone – Gizmodo

Drones could be stressing out wildlife, scientists suggest – Chelsea Harvey – Washington Post

Low-fat diets ‘better than cutting carbs’ for weight loss – James Gallagher – BBC News

Google’s Life Sciences division to build a miniature glucose tracker – Mona Lalwani – EnGadget

Why scientists got an alligator to inhale helium – Rachel Feltman – Washington Post

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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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