Author Archives: eliesbik

September 27, 2015

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General microbiome

Power Law Analysis of the Human Microbiome – Zhanshan Sam Ma – Molecular Ecology

Pregnancy and birth

Review: Probiotics and necrotizing enterocolitis – Paul Fleming – Pediatric Surgery International

Human oral microbiome

The efficacy of two oral hygiene regimens in reducing oral malodour: a randomised clinical trial – Magda Feres – International Dental Journal

Human respiratory tract microbiome

PhD Thesis: Investigating the host and bacterial factors in cystic fibrosis that promote persistence of infection in the lung – Daniel James Smith – University of Queensland

Human gut microbiome

Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants – Roberto Berni Canani – The ISME Journal

Review: Reciprocal interaction of diet and microbiome in inflammatory bowel diseases – Monika Schaubeck – Current Opinion in Gastroenterology

Review: Resistant starches for the management of metabolic diseases – Laure B. Bindels – Current Opinion in Clinical Nutrition & Metabolic Care

Animal models

Food availability affects the strength of mutualistic host–microbiota interactions in Daphnia magna – Martijn Callens – The ISME Journal

Animal microbiome

Microbial community assessment of mealworm larvae (Tenebrio molitor) and grasshoppers (Locusta migratoria migratorioides) sold for human consumption – J. Stoops – Food Microbiology

Indigenous microbiota and Leishmaniasis – Mateus Eustáquio de Moura Lopes – Parasite Immunology

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

Plant, root, and soil microbiome

Diversity patterns of Rhizobiaceae communities inhabiting soils, root-surfaces and nodules reveal a strong selection of rhizobial partners by legumes – Fabiola Miranda-Sánchez – Environmental Microbiology

Non-random species loss in bacterial communities reduces antifungal volatile production – W. H. Gera Hol – Ecology

Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment – Mohammad Bahram – The ISME Journal

Plant and root-endophyte assembly history: interactive effects on native and exotic plants – Benjamin A. Sikes – Ecology

Review: Plant and microbe genomics and beyond: potential for developing a novel molecular plant nutrition approach – Fernando Carlos Gómez-Merino – Acta Physiologiae Plantarum

Review: Engineering Microbiomes to Improve Plant and Animal Health – U.G. Mueller – Trends in Microbiology

Water microbiome

Metagenomic analysis of planktonic microbial consortia from a non-tidal urban-impacted segment of James River – Bonnie L. Brown – Standards in Genomic Sciences

Extremophile microbiome

Structure and function of natural sulphide-oxidizing microbial mats under dynamic input of light and chemical energy – Judith M Klatt – The ISME Journal

Emerging spatial patterns in Antarctic prokaryotes – Chun Wie Chong – Frontiers in Microbiology

Waste microbiology

Trace element and temperature effects on microbial communities and links to biogas digester performance at high ammonia levels – Maria Westerholm- Biotechnology for Biofuels

Food microbiology

Bacterial Diversity Analysis during the Fermentation Processing of Traditional Chinese Yellow Rice Wine Revealed by 16S rDNA 454 Pyrosequencing – Ruo-si Fang – Journal of Food Sciences

Isolation and characterization of bacteriocinogenic lactic bacteria from M-Tuba and Tepache, two traditional fermented beverages in México – Norma M. de la Fuente-Salcido – Food Science & Nutrition

Built environment microbiology

Diversity of Bacterial Biofilm Communities on Sprinklers from Dairy Farm Cooling Systems in Israel – Nahum Y. Shpigel – PLOS ONE

Microbial Ecology

Transient dynamics of competitive exclusion in microbial communities – Stilianos Louca – Environmental Microbiology

Metagenomics and bioinformatics

Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens – Bastian Greshake – Molecular Ecology Resources

Review: Recovering full-length viral genomes from metagenomes – Saskia Smits – Frontiers in Microbiology

Editorial: The main challenges that remain in applying high-throughput sequencing to clinical diagnostics – Michael Loeffelholz & Yuriy Fofanov – Expert Review of Molecular Diagnostics

Microbes in the News

uBiome Supports Oral Disease Prevention with Donations and Study – PR Web

Probiotic Formula Reverses Cow’s Milk Allergies by Changing Gut Bacteria of Infants – Lab Manager

Microbes and art

Microbe artwork shows the limits of antibiotics – University of Oxford

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September 25, 2015

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A crowd funding project to study mind and microbes, impact of early life gut colonization, microbial aspect to terroir, and khmer sequence analysis.

Crowd funding project: Are our bacteria making us depressed or anxious? – Philip Strandwitz – Experiment.com

Pregnancy and birth

Review: The impact of early life gut colonization on metabolic and obesogenic outcomes: what have animal models shown us? – J. G. Wallace – Journal of Developmental Origins of Health and Disease

Human gut microbiome

Chronic Kidney Disease: The Influence of CKD on Colonic Microbial Metabolism – Ruben Poesen – Journal of the American Society of Nephrology

Review: Could the beneficial effects of dietary calcium on obesity and diabetes control be mediated by changes in intestinal microbiota and integrity? – J. M. G. Gomes – British Journal of Nutrition

Animal models

The microbiota shifts the iron sensing of intestinal cells – Jean-Christophe Deschemin – The FASEB Journal

Plant, root, and soil microbiome

Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health – Zhong Wei – Nature Communications

Regional microbial signatures positively correlate with differential wine phenotypes: evidence for a microbial aspect to terroir – Sarah Knight – Scientific Reports

Methanogenic degradation of lignin-derived monoaromatic compounds by microbial enrichments from rice paddy field soil – Souichiro Kato – Scientific Reports

Food microbiology

A diagnosis of the microbiological quality of dehydrated bee-pollen produced in Brazil
A.A.M. De-Melo – Letters in Applied Microbiology

Waste microbiology

The biotransformation of brewer’s spent grain into biogas by anaerobic microbial communities – Dina V. Malakhova – World Journal of Microbiology and Biotechnology

Bioinformatics and metagenomics

The khmer software package: enabling efficient nucleotide sequence analysis – Michael R. Crusoe – F1000 research

Microbes in the news

That Stinky Cheese Is a Result of Evolutionary Overdrive – Carl Zimmer – New York Times

Bacteria are making it harder for would-be murderers – Alexandra Petri – Washington Post

Bacteria Hysteria

Note: research sponsored by Dettol: How your child’s teddy could trigger food poisoning: 80% of cuddly toys harbour harmful bacteria – while one in four are contaminated with faeces – Lizzie Parry – Daily Mail

Science, publishing, and career

How science fairs shaped my career – Rachel Yoho – Science

Bik’s Picks

Scientists discover new system for human genome editing – Phys.org

The truth about pigs – Henry Nicholls – BBC

1 1/2-pound baby born to Utah woman on cruise ship beats odds to survive – Lindsey Whitehurst – Associated Press
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September 24, 2015

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Human genetic variation and microbiome composition, turmeric & travel, Nicotiana recruitment, and microbial stress in the city.

General microbiome

Editorial: Host genetic architecture and the landscape of microbiome composition: humans weigh in – Andrew K Benson – Genome Biology

Host genetic variation impacts microbiome composition across human body sites
Ran Blekhman – Genome Biology

Database of host-pathogen and related species interactions, and their global distribution – Maya Wardeh – Scientific Data

Pregnancy and birth

The role of breast-feeding in infant immune system: a systems perspective on the intestinal microbiome – Paurush Praveen – Microbiome

The role of infection in miscarriage – Sevi Giakoumelou – Human Reproduction Update

Human gut microbiome

The Effect of Probiotics on Gut Microbiota during the Helicobacter pylori Eradication: Randomized Controlled Trial – Bumjo Oh – Helicobacter

Intestinal microbial communities associated with acute enteric infections and disease recovery – Pallavi Singh – Microbiome

Review: Advancing gut microbiome research using cultivation – Morten OA Sommer – Current Opinion in Microbiology

Human urinary tract microbiome

Re: The Microbiome of the Urinary Tract—A Role Beyond Infection – Alan J. Wein – The Journal of Urology

Animal models

Modulation of gut microbiota by berberine and metformin during the treatment of high-fat diet-induced obesity in rats – Xu Zhang – Scientific Reports

A small-molecule antivirulence agent for treating Clostridium difficile infection – Kristina Oresic Bender – Science Translational Medicine

Regulators of Gut Motility Revealed by a Gnotobiotic Model of Diet-Microbiome Interactions Related to Travel – Neelendu Dey – Cell

Animal microbiome

High-throughput DNA sequencing of the moose rumen from different geographical
location reveals a core ruminal methanogenic archaeal diversity and a differential
ciliate protozoal diversity – Suzanne Lynn Ishaq – Microbial Genomics

Microbial populations and fermentation profiles in rumen liquid and solids of Holstein cows respond differently to dietary barley processing – Barbara U. Metzler-Zebeli – Journal of Applied Microbiology

Culture based: Actinomycetes from the South China Sea sponges: isolation, diversity and potential for aromatic polyketides discovery – Zhiyong Li – Frontiers in Microbiology

Longitudinal study of the early-life fecal and nasal microbiotas of the domestic pig – Mackenzie Jonathan Slifierz – BMC Microbiology

Faecal microbiota characterisation of horses using 16 rdna barcoded pyrosequencing, and carriage rate of clostridium difficile at hospital admission – Cristina Rodriguez – BMC Microbiology

Essential Amino Acid Supplementation by Gut Microbes of a Wood-Feeding Cerambycid – Paul A. Ayayee – Environmental Entomology

Plant, root, and soil microbiome

RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere – Kalyan Chakravarthy Mynampati – Environmental Pollution

Vineyard soil bacterial diversity and composition revealed by 16S rRNA genes: Differentiation by geographic features – Kayla N. Burns – Soil Biology and Biochemistry

Nicotiana Roots Recruit Rare Rhizosphere Taxa as Major Root-Inhabiting Microbes – Muhammad Saleem – Plant Microbe Interactions

Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling – Feng Wang – Scientific Reports

The coupling of the plant and microbial catabolisms of phenanthrene in the rhizosphere of Medicago sativa – Anna Muratova – Journal of Plant Physiology

Contrasting soil bacterial community structure between the phyla Acidobacteria and Proteobacteria in tropical Southeast Asian and temperate Japanese forests – Naohiko T. Miyashita – Genes & Genetic Systems

Review: Ecological importance of soil bacterivores for ecosystem functions – Jean Trap – Plant and Soil

Editorial: Microbial ecology of hydrocarbon-polluted coastal sediments – Robert Duran – Environmental Science and Pollution Research

Waste microbiology

Identification of Bacteria Synthesizing Ribosomal RNA in Response to Uranium Addition During Biostimulation at the Rifle, CO Integrated Field Research Site – Lora R. McGuinness – PLOS ONE

Microbial ecology of hydrocarbon-polluted coastal sediments – Robert Duran – Environmental Science and Pollution Research

Built environment microbiome

Urban stress is associated with variation in microbial species composition-but not richness-in Manhattan – Aspen T Reese – ISME Journal

Microbiome of death

The Search for a Volatile Human Specific Marker in the Decomposition Process – E. Rosier – PLOS ONE

Bioinformatics and metagenomics

In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project’s reference genome database – Calum J. Walsh – BMC Microbiology

PhD thesis: Novel methods for comparing and evaluating single and metagenomic assemblies – Christopher M. Hill – University of Maryland

Microbes in the news

Metagenomic Sequencing Shows Changes in Healthy Gut Microbiome Pre- and Post-Antibiotics – Genome Web

Study shows whale microbiome shares characteristics with both ruminants and predators – Phys.org

Researchers isolate the ‘human smell of death’ – Elizabeth Pennisi – Science

Scientists find way to disarm deadly bacteria without destroying the good ones in your gut – Lena H. Sun – Washington Post

Science, publishing, and career

Failure to replicate the STAP cell phenomenon – Alejandro De Los Angeles – @nature

Make academic job advertisements fair to all: Too many university posts are given to men without proper competition – Mathias Wullum Nielsen – Nature

Gender-disparity study faces attack: A paper suggesting a Dutch grant scheme shows bias against women is criticized for a statistical flaw – Chris Woolston

Bik’s Picks

In the name of beauty: phasing out plastic microbeads found in skin scrubs – Nature

How Climate Change Shrank the Tongues of Long-Tongued Bumblebees – Ed Yong

Enamel evolved in the skin and colonized the teeth much later – EurekAlert

Giant Killer Lizards Lived Among Ice-Age Aussies – Discovery
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September 23, 2015

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Animal models

In mice: The outer mucus layer hosts a distinct intestinal microbial niche – Hai Li – Nature Communications

Animal microbiome

Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores – Jon G. Sanders – Nature Communications

Differences in Bacterial Community Structure in Two Color Morphs of the Hawaiian Reef Coral Montipora capitata – Amanda Shore-Maggio – Applied and Environmental Microbiology

Macaque feces: Non-random patterns in viral diversity – Simon J. Anthony – Nature Communications

Stable Associations Masked by Temporal Variability in the Marine Copepod Microbiome – Pia H. Moisander – PLOS ONE

Bacterial Diversity and Community Structure in the Pine Wood Nematode Bursaphelenchus xylophilus and B. mucronatus with Different Virulence by High-Throughput Sequencing of the 16S rDNA – Yang Xiang – PLOS ONE

Survey of Ixodes pacificus Ticks in California Reveals a Diversity of Microorganisms and a Novel and Widespread Anaplasmataceae Species – Mark W. Eshoo – PLOS ONE

Plant, root, and soil microbiome

Plant diversity drives soil microbial biomass carbon in grasslands irrespective of global environmental change factors – Madhav Prakash Thakur – Global Change Biology

Trait-based partner selection drives mycorrhizal network assembly – Pierre-Luc Chagnon – Oikos

Antifungal Rhizosphere Bacteria Can increase as Response to the Presence of Saprotrophic Fungi – Wietse de Boer – PLOS ONE

Exometabolite niche partitioning among sympatric soil bacteria – Richard Baran – Nature Communications

Water microbiome

The dynamical landscape of marine phytoplankton diversity – Marina Lévy – Journal of the Royal Society/Interface

Bioinformatics

PhyloMeasures: a package for computing phylogenetic biodiversity measures and their statistical moments – Constantinos Tsirogiannis and Brody Sandel – Ecography

RAMBO-K: Rapid and Sensitive Removal of Background Sequences from Next Generation Sequencing Data – Simon H. Tausch – PLOS ONE

Microbes in the news

You Produce a Microbial Cloud That Can Act Like an Invisible Fingerprint – Brian Handwerk – Smithsonian

Baleen Whale Shares Gut Microbiome Features with Land Herbivores, Carnivores – Genome Web

Bacteria Turns Santa Barbara Bird Refuge Pink – Alys Martinez – KEYT.com

Microbiome Diversity Affects Chemotherapy-Related Infection – Kate Johnson – Medscape

NASA’s Human Research Program studies how Microbes interact with Astronauts during Spaceflight – Amy Blanchett and Laurie Abadie – NASA

Stanford team re-engineers virus to deliver therapies to cells – Tom Abate – Stanford News

Science, publishing, and career

Four Proposals to Help Improve the Medical Research Literature – David Moher , Douglas G. Altman – PLOS Medicine

Gender contributes to personal research funding success in The Netherlands – Romy van der Lee and Naomi Ellemers – PNAS

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September 22, 2015

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Effect of hookworm infection on microbiome of celiac subjects, neutrophil ageing, altering the bone niche, and a personal microbial cloud.

Pregnancy and birth

Influence of a combination of probiotics on bacterial infections in very low birthweight newborns – Zlatka Kanic – Wiener klinische Wochenschrift

Microbiome of death

High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses – Seung Hak Yang – Genetics and Molecular Biology

Human respiratory tract microbiome

Investigation of bacterial repopulation after sinus surgery and perioperative antibiotics – Leah J. Hauser – International Forum of Allergy & Rhinology

Human oral microbiome

Comparison of Subgingival and Peri-implant Microbiome in Chronic Periodontitis – Zhang, Qian – Chinese Journal of Dental Research

The novel association between red complex of oral microbe and body mass index in healthy Japanese: a population based cross-sectional study – Kanae Matsushita – Journal of Clinical Biochemistry and Nutrition

Human gut microbiome

The relationship between faecal-associated and mucosal-associated microbiota in irritable bowel syndrome patients and healthy subjects – I. Rangel – Alimentary Pharmacology & Therapeutics

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

Effect of administering a multi-species probiotic mixture on the changes in fecal microbiota and symptoms of irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial – Hyuk Yoon – Journal of Clinical Biochemistry and Nutrition

Review: Improving healthspan via changes in gut microbiota and fermentation – Michael J. Keenan – AGE

Review: Gastric Microbiota – Gianluca Ianiro – Helicobacter

Thesis: High-resolution analysis of the human intestinal microbiota stability landscape – Tineka Blake – Aalto University

Animal models

An integrated metabonomics and microbiology analysis of host-microbiota metabolic interactions in rats with Coptis chinensis-induced diarrhea – Yemeng Li – RCS Advances

Microbiota from Obese Mice Regulate Hematopoietic Stem Cell Differentiation by Altering the Bone Niche – Yubin Luo – Cell Metabolism

The levonorgestrel-releasing intrauterine system is associated with delayed endocervical clearance of Chlamydia trachomatis without alterations in vaginal microbiota – E.R. Liechty – Pathogens and Disease

Goldfish: Correlations of Gut Microbial Community Shift with Hepatic Damages and Growth Inhibition of Carassius auratus Induced by Pentachlorophenol Exposure – Haifeng Kan – Environmental Science & Technology

Neutrophil ageing is regulated by the microbiome – Dachuan Zhang – Nature

Animal microbiome

Diversity analysis of diazotrophs associated with corals from Xisha and Sanya, South China Sea – Qingsong Yang – Aquatic Ecosystem Health & Management

Characterization of the Skin Microbiota in Italian Stream Frogs (Rana italica) Infected and Uninfected by a Cutaneous Parasitic Disease – Ermanno Federici – Microbes and Environments

Microbial diversity and activity in the Nematostella vectensis holobiont: insights from 16S rRNA gene sequencing, isolate genomes, and a pilot-scale survey of gene expression –
Jia Y. Har – Frontiers in Microbiology

Plant, root, and soil microbiome

Endophytic bacterial communities associated with two explant sources of Eucalyptus benthamii Maiden & Cambage – Natalia Pimentel Esposito-Polesi – World Journal of Microbiology and Biotechnology

Endospores, prokaryotes, and microbial indicators in arable soils from three long-term experiments – Paulina Tamez-Hidalgo – Biology and Fertility of Soils

Namib Desert dune/interdune transects exhibit habitat-specific edaphic bacterial communities – Sandra Ronca – Frontiers in Microbiology

Responses of aromatic-degrading microbial communities to elevated nitrate in sediments –
Meiying Xu – Environmental Science & Technology

Climate change and physical disturbance cause similar community shifts in biological soil crusts – Scott Ferrenberg – PNAS

Water / Extremophile microbiome

Patchy-distributed ciliate (Protozoa) diversity of eight polar communities as determined by 454 amplicon pyrosequencing – Jae-Ho Jung – Animal Cells and Systems

Protist communities in a marine oxygen minimum zone off Costa Rica by 454 pyrosequencing – H. Jing – Biogeosciences Discussions

Built environment microbiome

Humans differ in their personal microbial cloud – James F. Meadow – PeerJ

Waste microbiology

Relationship between bacterial diversity and environmental parameters during composting of different raw materials – Xueqin Wang – Bioresource Technology

The sociality of bioremediation: Hijacking the social lives of microbial populations to clean up heavy metal contamination – Siobhan O’Brien, Angus Buckling – EMBO Reports

Culturing oil sands microbes as mixed species communities enhances ex situ model naphthenic acid degradation – Marc A. Demeter – Frontiers in Microbiology

Microbial Ecology

Predicting microbial traits with phylogenies – Marta Goberna and Miguel Verdú – The ISME Journal

Bioinformatics and metagenomics

Metagenomic reconstructions of bacterial CRISPR loci constrain population histories – Christine L Sun – The ISME Journal

CCLasso: correlation inference for compositional data through Lasso – Huaying Fang – Bioinformatics

Computational methodology for predicting the landscape of the human–microbial interactome region level influence – Edgar D. Coelho – Journal of Bioinformatics and Computational Biology

Techniques

Targeted single molecule mutation detection with massively parallel sequencing – Mark T. Gregory – Nucleic Acids Research

Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures – Stefan A. Boers – Scientific Reports

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis – Thomas Briese – mBio

Microbes in the news

Wherever You Go, Your Personal Cloud Of Microbes Follows – Rob Stein – NPR

Former CEO knew about contamination, wrote “Just ship it”: 28 years for salmonella: Peanut exec gets groundbreaking sentence – Moni Basu – CNN

UGA microbiology researchers identify potential mechanism for neurodegenerative diseases – News Medical

Researchers find novel signature in the brains of children with cerebral malaria – EurekAlert

Science, publishing, and career

About annoying invitations to write papers in questionable journals and strategies how to handle those: You are invited to submit… – David Moher and Anubhav Srivastava – BMC Medicine

Bik’s Picks

8 trillion microbeads pollute U.S. aquatic habitats daily – Jareen Imam – CNN

Science Says This Is the Sound Giraffes Make – Alexandra Sifferlin – Time

I Am the Walrus: What 35,000 Walruses Tell Us About Our Future in Warming World – Miyoko Sakashita – Huffington Post

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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 13, 2015

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General microbiome

Prediction of relevant biomedical documents: a human microbiome case study – Paul Thompson – BioData Mining

Pregnancy and birth

High frequencies of antibiotic resistance genes in infants’ meconium and early fecal samples – M. J. Gosalbes – Journal of Developmental Origins of Health and Disease

Human gut microbiome

A Metagenomic Investigation of the Duodenal Microbiota Reveals Links with Obesity – Emmanouil Angelakis – PLOS ONE

Gut microbiota diversity predicts immune status in HIV-1 infection – Nowak, Piotr – AIDS

The human gut mycobiome: pitfalls and potentials-a mycologist’s perspective – Mallory J Suhr – Mycologia

Animal microbiome

Cloacal Microbiome Structure in a Long-Distance Migratory Bird Assessed Using Deep 16sRNA Pyrosequencing – Jakub Kreisinger – PLOS ONE

Plant, root, and soil microbiome

Plant Growth-Promoting Rhizobacteria Stimulate Vegetative Growth and Asexual Reproduction of Kalanchoe daigremontiana – Yong-Soon Park – The Plant Pathology Journal

Water / Extremophile microbiome

Activity and community structures of sulfate-reducing microorganisms in polar, temperate and tropical marine sediments – Alberto Robador – The ISME Journal

Ecology and application of haloalkaliphilic anaerobic microbial communities – João A.B. Sousa – Applied Microbiology and Biotechnology

Microbiological characterization of aquatic microbiomes targeting taxonomical marker genes and antibiotic resistance genes of opportunistic bacteria – Johannes Alexander – Science of the Total Environment

Bioinformatics and metagenomics

Predicting Microbial Interactions Using Vector Autoregressive Model with Graph
Regularization – Xingpeng Jiang – , IEEE/ACM Transactions on Computational Biology and Bioinformatics
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September 12, 2015

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Human gut microbiome reshaping by antibiotics, human gut microbiome and  blood lipids, periodontal disease in dogs, and microbial diversity in the presence of sequencing errors.

Human skin microbiome

Very small and not quite original study: Microbial Forensic Analysis of Bacterial Fingerprint by Sequence Comparison of 16S rRNA Gene – So-Yeon Lee – Forensic Research

Human gut microbioma

The initial state of the human gut microbiome determines its reshaping by antibiotics – Frédéric Raymond – The ISME Journal

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids – Jingyaun Fu – Circulation Research

Microbiome and Potential Targets for Chemoprevention of Esophageal Adenocarcinoma – Antonio Galvao Neto, M – Seminars in Oncology

Review: Gut Microbiome and the Development of Food Allergy and Allergic Disease – Benjamin T. Prince – Pediatrics Clinics of North America

Review: The Microbiome and Its Potential as a Cancer Preventive Intervention –
Scott J. Bultman – Seminars in Oncology

Animal microbiome

A longitudinal assessment of changes in bacterial community composition associated with the development of periodontal disease in dogs – Corrin Wallis- Veterinary Microbiology

Plant, root, and soil microbiome

Microbiote shift in the Medicago sativa rhizosphere in response to cyanotoxins extract exposure – Fatima El Khalloufi – Science of the Total Environment

Bacterial endophytes of sweet potato tuberous roots affected by the plant genotype and growth stage – Joana Montezano Marques – Applied Soil Ecology

Impact of grazing abandonment on plant and soil microbial communities in an Atlantic mountain grassland – A. Aldezabal – Applied Soil Ecology

Phyllosphere and carposphere bacterial communities in olive plants subjected to different cultural practices – Silvia Pascazio

Maize biochar addition rate influences soil enzyme activity and microbial community composition in a fluvo-aquic soil – Xiubin Wang – Applied Soil Ecology

Water microbiome

Microscopy- or DNA-based analyses: Which methodology gives a truer picture of stream-dwelling decomposer fungal diversity? – Isabel Fernandes – Fungal Ecology

Bioinformatics and metagenomics

Ten Simple Rules for a Computational Biologist’s Laboratory Notebook – Santiago Schnell – PLOS Computational Biology

Estimating and comparing microbial diversity in the presence of sequencing errors – Chun-Huo Chiu, Anne Chao – PeerJ Preprint

Poster abstract: How to design an efficient and robust pipeline for 16S rRNA-gene sequence analysis to improve our understanding on microbial communities? – Lucas Auer – Journées Ouvertes Biologie Informatique Mathématiques

Techniques

Another blast from the past: Simple fools guide to PCR v1 – Jonathan Eisen – Microbenet

Microbes in the news

Link between microbiota 
and piglet performance – All About Feed

Researchers compare the gut viromes of Malawian children with severe acute malnutrition – Christopher Packham – Medical Xpress

Keeping gut bacteria in balance could help delay age-related diseases, study finds – Stuart Wolpert – Medical Xpress

Gut Microbes Associated With HDL, Triglycerides, and BMI – Becky McCall – MedScape

How Bacteria Control Your Cholesterol – Alice Park – Time

Why You Should Not Wear Contact Lenses – Health Impact News

Science, publishing, and career

Eva Harris: making science democratic, and sustainable – The Lancet

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September 11, 2015

Posted on by

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 10, 2015

Posted on by

Plaque microbiome model to predict caries development, ocular microbiota and Sjögren’s, and aging  fungus cultivating termites.

Events

Free workshop at #UCDavis: “Microbial genomics and transcriptomics hands-on”, Sep 24-25 – Jonathan Eisen – Phylogenomics

Human skin and eye microbiome

TSP-1 Deficiency Alters Ocular Microbiota: Implications for Sjögren’s Syndrome Pathogenesis – Terzulli Marielle – Journal of Ocular Pharmacology and Therapeutics

Human oral microbiome

See “Telltale Mouth Microbes” article below, featuring yours truly: Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota – Fei Teng – Cell Host & Microbe

Human respiratory microbiome

High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in bronchoalveolar lavage fluid in patients with ventilator-associated pneumonia – Xiao-Jun Yang – Drug Design, Development and Therapy

Bacteria in the CF Lung: Isolation Drives Diversity – Pablo Manfredi – Cell Host & Microbe

Human reproductive tract microbiome

Cervicovaginal microbiome dysbiosis is associated with proteome changes related to alterations of the cervicovaginal mucosal barrier – H Borgdorff – Mucosal Immunology

Human gut microbiome

The Long-term Efficacy and Safety of Fecal Microbiota Transplant for Recurrent, Severe, and Complicated Clostridium difficile Infection in 146 Elderly Individuals – Agrawal, Manas – Journal of Clinical Gastroenterology

Gut Microbiome Composition in Young Nicaraguan Children During Diarrhea Episodes and Recovery – Sylvia Becker-Dreps – Am J Trop Med Hyg

PhD Thesis: Impaired Gut Microbial Community Development in Undernourished Children – Sathish Subramanian – Washington University

Review: Frenemies: Signaling and Nutritional Integration in Pathogen-Microbiota-Host Interactions – Elizabeth A. Cameron, Vanessa Sperandio – Cell Host & Microbe

Review: Fecal microbiota transplantation as therapy for inflammatory bowel disease: A systematic review and meta-analysis – Ruben J. Colman – Journal of Crohn’s and Colitis

Review: Candida albicans commensalism in the gastrointestinal tract – B. Anne Neville – Yeast Research

Review: Fecal microbiota analysis: an overview of sample collection methods and sequencing strategies – Vincent Thomas – Future Microbiology

Review: The interaction of commensal intestinal bacteria with helminth parasites – Mario M. Zaiss – Parasite Immunology

Animal microbiome

Age polyethism drives community structure of the bacterial gut microbiota in the fungus-cultivating termite Odontotermes formosanus – Hongjie Li – Environmental Microbiology

Diet is the primary determinant of bacterial community structure in the guts of higher termites – Aram Mikaelyan – Molecular Ecology

Isolation of aerobic cultivable cellulolytic bacteria from different regions of the gastrointestinal tract of giant land snail Achatina fulica – Guilherme L. Pinheiro – Frontiers in Microbiology

Plant, soil, and root microbiome

Fungal endophyte Phomopsis liquidambari affects nitrogen transformation processes and related microorganisms in the rice rhizosphere – Bo Yan – Frontiers in Microbiology

Soil fungi for mycoremediation of arsenic pollution in agriculture soils – Manvi Singh
– Journal of Applied Microbiology

Woody plant encroachment, and its removal, impact bacterial and fungal communities across stream and terrestrial habitats in a tallgrass prairie ecosystem – Allison M. Veach – Microbiology Ecology

Review: The role of microorganisms in the ecological functions of soils – T. G. Dobrovol’skaya – Eurasian Soil Science

Water microbiome

Studying composition of bacteriobenthic communities in the sediments of water ecosystems by fatty acid markers – N. G. Sherysheva – Aquatic Microbiology

Extremophiles

Microbial life in Bourlyashchy, the hottest thermal pool of Uzon Caldera, Kamchatka -Nikolay A. Chernyh – Extremophiles

Microbes of the built environment

Metabolomic and high-throughput sequencing analysis – modern approach for the assessment of biodeterioration of materials from historic buildings – Beata Gutarowska – Frontiers in Microbiology

Metagenomics and bioinformatics

Fragmentation and coverage variation in viral metagenome assemblies, and their effect in diversity calculations – Rodrigo García-López – Frontiers in Bioengineering and Biotechnology

Tentacle: distributed quantification of genes in metagenomes – Fredrik Boulund – GigaScience

Potential and pitfalls of eukaryotic metagenome skimming: A test case for lichens –
Bastian Greshake – Molecular Ecology Resources

Techniques

Effects of freezing storage on the DNA extraction and microbial evaluation from anaerobic digested sludges – Valeria Romanazzi – BMC Research Notes

Microbes in the news

Telltale Mouth Microbes- The composition of the plaque microbiome can reveal a child’s risk of dental caries months before the decay appears, according to a study. – Jyoti Madhusoodanan – The Scientist

Researcher Succumbs To Cystic Fibrosis, Leaves Unique Investigative Legacy – Charles Moore – Cystic Fibrosis News Today

uBiome Extends Reach of Microbiome Testing Through Global Ambassador Program – PR Web

Get the Poop on Organisms Living in Your Gut With a New Consumer Laboratory Test Offered by American Gut and uBiome – Dark Daily

“A diversity of gifts”: article about the MBL Microbial Diversity course – Jonathan Eisen – Microbe.net

Nanomesh dressings may draw bacteria from chronic wounds – Ben Coxworth – GizMag

Purple bacteria signal zinc deficiency – James Urquhart – Chemistry World

Professor pursues bacteria-to-fuel research abroad: Dr. Galyna Kufryk spent part of the summer studying cyanobacteria at the Institut Pasteur in Paris – Janie Magruder – Grand Canyon University

Bacteria in Overdrive: a key organism in the ocean’s food web will start reproducing at high speed as carbon dioxide levels rise – Robert Perkins – USC Dornsife

Bacteria Hysteria

The Most Bacteria-Infested Places on an Airplane – Rachael Schultz – Shape

Microbes and art

AMNH to present The Secret World Inside You exhibit, 11/4 – Broadway World

Science, publishing, and career

Q&A: The academic satirist: Jorge Cham wowed graduate students with The PhD Movie in 2011 – Zoë Corbyn – Nature

Gender balance: Women are funded more fairly in social science – Paul J. Boyle – Nature
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