Category Archives: Water microbiome

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

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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 10, 2015

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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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September 8, 2015

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How Bifidobacterium species digest human milk oligosaccharides, yeast species in floral nectar, and microbes of the cryosphere.

Pregnancy and birth

Comparative transcriptomics reveals key differences in the response to milk oligosaccharides of infant gut-associated bifidobacteria – Daniel Garrido – Scientific Reports

Human oral microbiome

Dental caries-not just holes in teeth! A perspective – William H. Bowen – Molecular Oral Microbiology

Progress in oral personalized medicine: contribution of ‘omics’ – Ingrid Glurich – Journal of Oral Microbiology

Human gut microbiome

Editorial: Modeling the Context-Dependent Associations between the Gut Microbiome, Its Environment, and Host Health – Thomas J. Sharpton – mBio

Review: Gut Microbiota Dysbiosis in Obesity-Linked Metabolic Diseases and Prebiotic Potential of Polyphenol-Rich Extracts – Fernando F. Anhê – Current Obesity Reports

Review: The gut microbiota and host health: a new clinical frontier – Julian R Marchesi – Gut

Animal models

Distinct but Spatially Overlapping Intestinal Niches for Vancomycin-Resistant Enterococcus faecium and Carbapenem-Resistant Klebsiella pneumoniae – Silvia Caballero – PLOS Pathogens

An Overview of Typical Infections of Research Mice: Health Monitoring and Prevention of Infection – James R. Fahey – Current Protocols in Mouse Biology

Editorial: The bug eye bandits – Yvonne Bordon – Nature Reviews Immunology

Plant, root, and soil microbiome

Species coexistence in simple microbial communities: unravelling the phenotypic landscape of co-occurring Metschnikowia species in floral nectar – María I. Pozo – Environmental Microbiology

Unveiling the metabolic potential of two soil-derived microbial consortia selected on wheat straw – Diego Javier Jiménez – Scientific Reports

Crop rotation of flooded rice with upland maize impacts the resident and active methanogenic microbial community – Björn Breidenbach – Environmental Microbiology

Water microbiome

Methane and microbial dynamics in the Gulf of Mexico water column – Chrisoulla Rakowski – Frontiers in Marine Science

Transformation of Organic Matter by Microbial Community in Sediments of Lake Baikal under Experimental Thermobaric Conditions of Protocatagenesis – Olga N. Pavlova – Geomicrobiology Journal

Extremophiles

Metagenomic analysis reveals that modern microbialites and polar microbial mats have similar taxonomic and functional potential – Richard A. White III – Frontiers in Microbiology

Review: Microbial ecology of the cryosphere: sea ice and glacial habitats – Antje Boetius – Nature Reviews Microbiology

Metagenomics and bioinformatics

ConStrains identifies microbial strains in metagenomic datasets – Chengwei Luo – Nature Biotechnology

Review: High-throughput bacterial functional genomics in the sequencing era – Andrew N Gray – Current Opinion in Microbiology

Techniques

Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification – Yusi Fu – PNAS

Microbes in the news

Seal fur and Arctic bacteria leach toxic mercury into waters – Joshua Sokol – New Scientist

Time to Give Up Showers and Spray Yourself With a Coating of Live Bacteria –
Madeleine Davies – Jezebel

A Look Inside the Lunch Boxes of Diet & Exercise Researchers – Ann Marie Awad – WRKF

Poo transplants can eliminate two superbugs from the gut: mice study – Eliza Berlage – The Conversation

Genetic Factors Drive Roles of Gut Bacteria in Diabetes and Obesity – News Wise

Bik’s Picks

Mercury offloaded in Northern elephant seal hair affects coastal seawater surrounding rookery – Jennifer M. Cossaboon – PNAS

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September 7, 2015

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Human skin microbiome

Skin microbiota-associated inflammation precedes autoantibody induced tissue damage in experimental epidermolysis bullosa acquisita – Christoph T. Ellebrecht – Journal of Autoimmunity

Human stomach and gut microbiome

Review: The stomach in health and disease – R H Hunt – Gut

Review: Intestinal microbiota and ulcerative colitis – Toshifumi Ohkusa – Journal of Infection and Chemotherapy

Animal microbiome

Cryptic diversity, reproductive isolation and cytoplasmic incompatibility in a classic biological control success story – Marco Gebiola – Biological Journal of the Linnean Society

Plant, root, and soil microbiome

Fungal community shifts in structure and function across a boreal forest fire chronosequence – Hui Sun – Applied and Environmental Microbiology

Patterns of endemism and habitat selection in coalbed microbial communities
Christopher E. Lawson – Applied and Environmental Microbiology

Geogenic factors as drivers of microbial community diversity in soils overlying polymetallic deposits – Frank Reith – Applied and Environmental Microbiology

Abundance of Antibiotic Resistance Genes in Bacteriophage Following Soil Fertilization With Dairy Manure or Municipal Biosolids, and Evidence for Potential Transduction – Joseph Ross – Applied and Environmental Microbiology

Water microbiome

Human-associated fecal qPCR measurements and simulated risk of gastrointestinal illness in recreational waters contaminated with raw sewage – Alexandria B. Boehm – Environmental Science & Technology Letters

Built environment microbiome

Coexistence of lactic acid bacteria and potential spoilage microbiota in a dairy-processing environment – Giuseppina Stellato – Applied and Environmental Microbiology

Microbes in the news

Goodbye showers-bacteria spray improves health? – Fox2

Researchers expanding use of poliovirus for cancer treatment – Nidhila Masha – Duke Chronicle

Bacteria Advisories Issued for 18 beaches along Texas Coast – KiiiTV

Bacteria could threaten pistachios in NM – Angela Simental – Albuquerque Journal

Possible Key in Virus, Cancer Research Identified – Kathleen Haughney – Labmanager

Bacteria Hysteria

Faecal matter on the TV remote, bodily fluids on bed linens and drinking glasses wiped with a filthy cloth: The dirtiest areas of a hotel room revealed – Chris Kitching – Daily Mail

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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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