Category Archives: Extremophiles

September 13, 2015

Posted on by

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
[hr]

September 8, 2015

Posted on by

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

[hr]

August 30, 2015

Posted on by

Pregnancy and birth

Fecal Microbial Community Structure Is Stable over Time and Related to Variation in Macronutrient and Micronutrient Intake in Lactating Women – Janae M Carrothers – The Journal of Nutrition

Human oral microbiome

Comparison between Clinical Aspects and Salivary Microbial Profile of Children with and without Early Childhood Caries: A Preliminary Study – Neves AB – Journal of Clinical Pediatric Dentistry

Human gut microbiome

Systematic review: microbial dysbiosis and nonalcoholic fatty liver disease – A. Wieland – Alimentary Pharmacology & Therapeutics

Animal and bioreactor models

Effect of Bifidobacterium thermophilum RBL67 and fructo-oligosaccharides on the gut microbiota in Göttingen minipigs – Sabine A. Tanner – British Journal of Nutrition

Interactions between Drosophila and its natural yeast symbionts—Is Saccharomyces cerevisiae a good model for studying the fly-yeast relationship? – Don Hoang – PeerJ

Differential responses of gut microbiota to the same prebiotic formula in oligotrophic and eutrophic batch fermentation systems – Wenmin Long – Scientific Reports

Animal microbiome

Structure of Manila Clam (Ruditapes philippinarum) Microbiota at the Organ Scale in Contrasting Sets of Individuals – Guillaume Meisterhans – Invertebrate Microbiology

Plant, root, and soil microbiome

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

Comparison of soil microbial communities inhabiting vineyards and native sclerophyllous forests in central Chile – Luis E. Castañeda – Ecology and Evolution

Diversity and distribution of bacterial community in the coastal sediments of Bohai Bay, China – Liping Wang – Acta Oceanologica Sinica

The impact on the soil microbial community and enzyme activity of two earthworm species during the bioremediation of pentachlorophenol-contaminated soils – Zhong Lin – Journal of Hazardous Materials

Water microbiome

Terrestrial origin of bacterial communities in complex boreal freshwater networks – Clara Ruiz-González – Ecology Letters

How are microbial and detrital sources partitioned among and within gastropods species at East Pacific Rise hydrothermal vents? – Sylvie M. Gaudro – Marine Ecology

Extremophile microbiome

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

Adaptation strategies of endolithic chlorophototrophs to survive the hyperarid and extreme solar radiation environment of the Atacama Desert – Jacek Wierzchos – Frontiers in Microbiology

Microbial biogeography of permafrost thaw ponds across the changing northern landscape – Jérôme Comte – Ecography

Food microbiology

Microbiota of Minas cheese as influenced by the nisin producer Lactococcus lactis subsp. lactis GLc05 – Luana Martins Perin – International Journal of Food Microbiology

Built Environment microbiology

Microbiome interplay: plants alter microbial abundance and diversity within the built environment – Alexander Mahnert – Frontiers in Microbiology

Bioinformatics

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways – Zachary A. King – PLOS Biology

Microbes in the news

Scientists Send Kombucha to Space in Search for Extraterrestrial Life – Kasandra Brabaw – Space.com

How Fats Influence the Microbiome – Kate Yandell – The Scientist

Fish oil diet modifies gut bacteria to boost health – News Medical

Soupy bacteria clogs Missisquoi Bay: “When it rots, it stinks bad” – Joel Banner Baird – Burlington Free Press

Bacteria Hysteria

Caveat: Sponsored by a make-up company. I cannot find any publication associated with this article either. Out of date make-up can contain lethal bacteria, London Met scientist finds – London Metropolitan University

‘There’s no way of knowing what fungus or bacteria is left on it’: Medical expert slams bizarre website that buys USED make-up from beauty lovers – before selling it again – Catherine Townsend – Daily Mail

Science, publishing, and career

The most important tasks for peer reviewers evaluating a randomized controlled trial are not congruent with the tasks most often requested by journal editors – Anthony Chauvin – BMC Medicine
[hr]

August 27, 2015

Posted on by

Microbiome general/other

A comprehensive repertoire of prokaryotic species identified in human beings – Perrine Hugon – The Lancet Infectious Diseases

Linking the relevance of microbiota composition shifts with intestinal health disorders: a complex issue – Filip Boyen – Veterinary Journal

Effects of Long Term Antibiotic Therapy on Human Oral and Fecal Viromes – Shira R. Abeles – PLOS ONE

High-throughput sequencing of 16S rDNA amplicons characterizes bacterial composition in cerebrospinal fluid samples from patients with purulent meningitis– Aicui Liu – Drug Des Devel Ther

Pregnancy and birth microbiome

Several abstracts in Placenta:

 

Human oral microbiome

Pyrosequencing analysis of apical microbiota of teeth with persistent apical periodontitis – Yifan Ping – Journal of Dental Sciences

Human gut microbiome

Structure and function of the healthy pre-adolescent pediatric gut microbiome – Emily B. Hollister – Microbiome

Are proton pump inhibitors affecting intestinal microbiota health? – S. Melgar – Gastroenterology

Microbiome models

Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling – Robert Caesar – Cell Metabolism

Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development – Adam R Burns – The ISME Journal

Animal microbiome

The microbial community structure of the cotton rat nose – Diego Chaves-Moreno – Environmental Microbiology Reports

Water / Extremophile microbiome

Freshwater ice as habitat: partitioning of phytoplankton and bacteria between ice and water in central European reservoirs – Robert M.L. McKay – Environmental Microbiology Reports

High protists diversity in the plankton of sulfurous lakes and lagoons examined by 18s rRNA gene sequence analyses – Xavier Triadó-Margarit – Environmental Microbiology Reports

Bioreactor microbiology

Housefly Larvae Vermicomposting Efficiently Attenuates Antibiotic Resistant Genes in Swine Manure Coupled with Distinct Bacterial Population Change – Hang Wang – Applied and Environmental Microbiology

Techniques

A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing – Wenke Smets – PeerJ PrePrints

Mock communities highlight the diversity of host-associated eukaryotes – Laura Wegener Parfrey – Molecular Ecology

Microbes in the news

Lab experiments question popular measure of ancient ocean temperatures – Hannah Hickey – University of Washington

Is your spacecraft contaminating the universe? – Jonathan Eisen – Microbe.net

Birmingham Zoo closes aviary after bacteria found in bird – Washington Times

Science, publishing, and career

EntryPoint! places students with disabilities on STEM tracks – Becky Ham – Science

[hr]

August 25, 2015

Posted on by

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
[hr]

August 15, 2015

Posted on by

Here is your Saturday edition of the Digest. Four papers today about Arctic water and soil microbes, oral bacteria in placentas, using hand microbiomes to identify human ethnicities, and machine learning classifiers give insights in bacterial vaginosis.

Pregnancy and birth microbiome

Oral bacteria in placental tissues: Increased molecular detection in pregnant periodontitis patients – Vanessa Blanc – Oral Diseases

Human skin microbiome

Hand bacteria as an identifier: a biometric evaluation – Amanda B. Holbert – Network Modeling Analysis in Health Informatics and Bioinformatics

Minireview: From Head to Toe: Mapping Fungi across Human Skin – Tim Sandle – EC Microbiology

Human respiratory microbiome

Impact of cigarette smoking on the middle meatus microbiome in health and chronic rhinosinusitis – Vijay R. Ramakrishnan – International Forum of Allergy & Rhinology

Human gut microbiome

Metagenomic Analysis of Crohn’s Disease Patients Identifies Changes in the Virome and Microbiome Related to Disease Status and Therapy, and Detects Potential Interactions and Biomarkers – Pérez-Brocal, Vicente – Inflammatory Bowel Diseases

Animal models

SIV-infection-driven changes of pattern recognition receptor expression in mesenteric lymph nodes and gut microbiota dysbiosis – Tiffany W. Glavan – Journal of Medical Primatology

Plant, root, and soil microbiome

Diazotrophic bacilli isolated from the sunflower rhizosphere and the potential of Bacillus mycoides B38V as biofertiliser – A. Ambrosini – Annals of Applied Biology

Relationships between Oak powdery mildew incidence and severity and commensal fungi – E. T. Topalidou – Forest Pathology

The core microbiome bonds the Alpine bog vegetation to a transkingdom metacommunity – Anastasia Bragina – Molecular Ecology

Warming reduces the cover and diversity of biocrust-forming mosses and lichens, and increases the physiological stress of soil microbial communities in a semi-arid Pinus halepensis plantation – Fernando T. Maestre – Frontiers in Microbiology

Microbial Mineral Colonization Across a Subsurface Redox Transition Zone – Brandon Converse – Frontiers in Microbiology

Mutabilis in mutabili: Spatiotemporal dynamics of a truffle colony in soil – Milan Gryndler – Soil Biology and Biochemistry

Water microbiome

Bacterioplankton community shifts associated with epipelagic and mesopelagic waters in the Southern Ocean – Zheng Yu – Scientific Reports

Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period – Anne Poste – Frontiers in Microbiology

Extremophile microbiome: Arctic edition

Microbial activity is not always limited by nitrogen in Arctic tundra soils – Caroline Melle – Soil Biology and Biochemistry

Arctic soil microbial diversity in a changing world – Aimeric Blaud – Research in Microbiology

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

Diversity of planktonic microorganisms in the Arctic Ocean – Carlos Pedrós-Alió – Progress in Oceanography

Waste treatment microbiology

Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge – Ariane Bize – Proteomics

Bioinformatics

Machine learning classifiers provide insight into the relationship between microbial communities and bacterial vaginosis – Daniel Beck – BioData Mining

AmpliSAS: a web server for multilocus genotyping using next-generation amplicon sequencing data – Alvaro Sebastian – Molecular Ecology Resources

Science, publishing, and career

My alma mater, Utrecht University was again voted as the best Dutch university! Academic Ranking of World Universities 2015 – Shanghai Ranking

Microbes in the news

The Microbial Discovery Box: a hands-on activity for science teachers – ASM

Young scientists dreaming big: internship presentation competitions – Uganda Virus Research Institute

Infectious Diseases Like It Hot: How Climate Change Helps Cholera and Salmonella Outbreaks – Marlene Cimons – Think Progress

Before an Animal Disease Becomes a Human Epidemic – Cari Romm – The Atlantic

The dangers of eating snakes: Gauteng pastor encouraged his congregation to eat hair and snakes.

Bik’s Picks

Air Problem Is Worse Than You Think – James Fallows – The Atlantic

Georgia court weighs destiny of 18 captured beluga whales – Rich McKay – Reuters

Los Angeles Throws 96M Balls At California’s Drought Problem – Science Daily

[hr]

August 8, 2015

Posted on by

Lung and oral microbiomes in setting of HIV infection, cell biology of the plant–microbe interface, deep see prokaryotes, bacterial succession during grape fermentation, and correcting amplicon errors with Dada2.

Pregnancy and birth microbiome

Is abnormal vaginal microflora a risk factor for intrauterine fetal growth restriction? – Natalija Vedmedovska – Asian Pacific Journal of Reproduction

Multiple Opportunistic Pathogens, but Not Pre-existing Inflammation, May Be Associated with Necrotizing Enterocolitis – Steven T. Leach – Digestive Diseases and Sciences

Review: Nutrient availability, the microbiome and intestinal transport during pregnancy – Stuart Astbury – Applied Physiology, Nutrition, and Metabolism

Human oral and lung microbiome

Multi-center Comparison of Lung and Oral Microbiomes of HIV-infected and HIV-uninfected Individuals – James M. Beck – American Journal of Respiratory and Critical Care Medicine

Review: Microbial protection and virulence in periodontal tissue as a function of polymicrobial communities: symbiosis and dysbiosis – Frank A. Roberts and Richard P. Darveau – Periodontology 2000

Needs assessment for emerging oral microbiome knowledge in dental hygiene education – R. Constance Wiener – Journal of Epidemiological Research

Human reproductive microbiome

Is abnormal vaginal microflora a risk factor for intrauterine fetal growth restriction? – Natalija Vedmedovska – Asian Pacific Journal of Reproduction

Human gut microbiome

Alterations of mucosal microbiota in the colon of patients with inflammatory bowel disease revealed by real time polymerase chain reaction amplification of 16S ribosomal ribonucleic acid – Jayakanthan Kabeerdoss – Indian J Med Res

An In Vitro Method to Assess Soil Arsenic Metabolism by Human Gut Microbiota: Arsenic Speciation and Distribution – Naiyi Yin – Environmental Science & Technology

Review: Does a low FODMAP diet help IBS? – Drug and Therapeutics Bulletin

Microbiome models

Modulation of intestinal microbiota in mice by kefir administration – Dong-Hyeon Kim – Food Science and Biotechnology

High nutrient availability reduces the diversity and stability of the equine caecal microbiota – Naja C. K. Hansen – Microbial Ecology in Health & Disease

Impact of Dietary Fiber/Starch Ratio in Shaping Cecal Microbiota in Rabbits – YanLi Zhu – Canadian Journal of Microbiology

Animal microbiome

Electrical Retrieval of Living Microorganisms from Cryopreserved Marine Sponges Using a Potential-Controlled Electrode – Sumihiro Koyama – Marine Biotechnology

PhD Thesis: Reproduction, Sex Ratio and Bacterial Communities of the Coffee Berry Borer Hypothenemus Hampei F. (Coleoptera: Curculionidae) – Mariño Cárdenas – Universidad de Puerto Rico

Effect of starch source (corn, oats or wheat) and concentration on fermentation by equine fecal microbiota in vitro – Brittany E. Harlow – Journal of Applied Microbiology

Role of peptidases of the intestinal microflora and prey in temperature adaptations of the digestive system in planktivorous and benthivorous fish – V. V. Kuz’mina – Fish Physiology and Biochemistry

Plant, root, and soil microbiome

Environmental conditions rather than microbial inoculum composition determine the bacterial composition, microbial biomass and enzymatic activity of reconstructed soil microbial communities – Weibing Xun – Soil Biology and Biochemistry

Editorial: Introduction to a Virtual Special Issue on cell biology at the plant–microbe interface – Ralph Panstruga and Hannah Kuhn – New Phytologist

Influence of 34-years of fertilization on bacterial communities in an intensively cultivated black soil in northeast China – Jing Zhou – Soil Biology and Biochemistry

Functional and structural responses of methanogenic microbial communities in Uruguayan soils to intermittent drainage – Yang Ji – Soil Biology and Biochemistry

Effects of pasture management on soil fertility and microbial communities in the semi-arid grasslands of Inner Mongolia – Jun Liu – Journal of Soils and Sediments

Antibiotic resistance differentiates Echinacea purpurea endophytic bacterial communities with respect to plant organs – Alessio Mengoni – Research in Microbiology

Effect of combined microbes on plant tolerance to Zn–Pb contaminations – Anna Ogar – Environmental Science and Pollution Research

From mesophilic to thermophilic digestion: the transitions of anaerobic bacterial, archaeal, and fungal community structures in sludge and manure samples – Weimin Sun – Applied Microbiology and Biotechnology

Water microbiome

Metagenome-based diversity analyses suggest a significant contribution of non-cyanobacterial lineages to carbonate precipitation in modern microbialites – Aurélien Saghaï – Frontiers in Microbiology

Thesis: Geobiological interactions of archaeal populations in acidic and alkaline geothermal springs of Yellowstone National Park, WY, USA – Jacob Preston Beam – Montana State University

Global diversity and biogeography of deep-sea pelagic prokaryotes – Guillem Salazar – ISME Journal

Built environment microbiology

Halophilic microbial communities in deteriorated buildings – Justyna Adamiak – World Journal of Microbiology and Biotechnology

Food microbiology

Insights into the bacterial community and its temporal succession during the fermentation of wine grapes – Hailan Piao – Frontiers in Microbiology

Identification of key microorganisms involved in Douchi fermentation by statistical analysis and their use in an experimental fermentation – Chen Chen – Journal of Applied Microbiology

In vitro fermentation of lupin seeds (Lupinus albus) and broad beans (Vicia faba): dynamic modulation of the intestinal microbiota and metabolomic output – Patricia Gullón – Food & Function

Bioinformatics

DADA2: High resolution sample inference from amplicon data – Benjamin J Callahan

Transcriptomics

Molecular and chemical dialogues in bacteria-protozoa interactions – Chunxu Song – Scientific Reports

Techniques

Methods for Improving Human Gut Microbiome Data by Reducing Variability through Sample Processing and Storage of Stool – Monika A. Gorzelak – PLOS ONE

Microbes in the News

Prestigious Japanese university comes up with cheesecake … made with Gorilla bacteria! – RocketNews

Lambton College research project proves successful in eliminating bacteria in firefighting gear – Lambton College

Where the sausage gets made – Holly Ganz – MicroBEnet

Calgary diseases expert on the importance of studying our guts – The Globe and Mail

Bik’s Picks

Creepers’ peepers: Why animals’ pupils have different shapes – Nicholas St. Fleur – Seattle Times

Venomous frogs discovered during painful scientific mishap: Frogs head-butt enemies with their spines to inject toxic venom – CBC News

ISS Astronauts to Sample Leafy Greens Grown on Space Station – NDTV

[hr]

August 1, 2015

Posted on by

So many new papers, so here is another Saturday installment of The Digest. Several papers on microbiome during pregnancy or the first months of life, ear infections, having older siblings, rhizosphere on volcanic islands, and aquatic fungal communities.

General human microbiome

A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota – David J. Roach – PLOS Genetics

Opinion: The human–microbe metaorganism, evolution and extraterrestrial colonization – Leonard A Mermel – Future Microbiology

Frailty and the Microbiome – Meehan C.J. – Frailty in Aging

Pregnancy and birth microbiome

Secretor Status Is Strongly Associated with Microbial Alterations Observed during Pregnancy – Himanshu Kumar – PLOS ONE

Longitudinal Survey of Microbiota in Hospitalized Preterm Very Low Birth Weight Infants – Patel, Aloka L. – Journal of Pediatric Gastroenterology & Nutrition

Lactation and Intestinal Microbiota: How Early Diet Shapes the Infant Gut
Felicia Goldsmith – Journal of Mammary Gland Biology and Neoplasia

DGGE: Distinctive Intestinal Lactobacillus Communities in Six-Month-Old Infants From Rural Malawi and South-Western Finland – Aakko, Juhani – Journal of Pediatric Gastroenterology & Nutrition

Early Gut Colonization with Lactobacilli and Staphylococcus in Infants: the Hygiene Hypothesis Extended – Salminen, Seppo – Journal of Pediatric Gastroenterology & Nutrition

Association between positive urine cultures and necrotizing enterocolitis in a large cohort of hospitalized infants – Leslie C. Pineda – Early Human Development

Human oral microbiome

Strains of Enterococcus faecalis differ in their ability to coexist in biofilms with other root canal bacteria – L. E. Chávez de Paz – International Endodontic Journal

Human respiratory microbiome

Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation – Elise S. Cowley – mBio

Human skin and ear microbiome

The microbiome of otitis media with effusion in Indigenous Australian children – Jake Jervis-Bardy – International Journal of Pediatric Otorhinolaryngology

Review: Probiotics in personal care products – Mei-Chiung Jo Huang – Microbiology Discovery

Human gut microbiome

Having older siblings is associated with gut microbiota development during early childhood – Martin Frederik Laursen – BMC Microbiology

Serum Trimethylamine-N-Oxide is Elevated in CKD and Correlates with Coronary Atherosclerosis Burden – Jason R. Stubbs – Journal of the American Society of Nephrology

Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer – Zhiguang Gao – Molecular Medicine Reports

A Survey on the Developmental Intestinal Microbiota Research in China: the history, funding, and frontiers of gut bacteria – Hui Min Chen – Journal of Digestive Diseases

Review: Gut microorganisms as promising targets for the management of type 2 diabetes – Nathalie M. Delzenne – Diabetologia

Microbiome models

Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection – Andrew Leber – PLOS ONE

Evaluation of mucositis induced by irinotecan after microbial colonization in germ-free mice – Silvia H S P Pedroso – Microbiology

Animal microbiome

Exploring the microbial diversity of the distal intestinal lumen and mucosa of farmed rainbow trout Oncorhynchus mykiss (Walbaum) using next generation sequencing (NGS) – Philip P. Lyons – Aquaculture Research

Plant, root, and soil microbiome

Rhizosphere on volcanic islands: Metagenomic analysis of soil fungal communities on Ulleungdo and Dokdo Islands – Yoon-Jong Nam – The Journal of General and Applied Microbiology

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

Vulnerability of Soil and Its Associated Organic Matter to Degradation in a Subtropical Region: A Study From São Paulo State, Brazil – Alexandre Marco da Silva – Environment Quality Management

Effects of historical logging on soil microbial communities in a subtropical forest in southern China – Piao Song – Plant and Soil

Effects of rotifers, copepods and chironomid larvae on microbial communities in peatlands – Tomasz Mieczan – European Journal of Protistology

Methanogenic microbial community of the Eastern Paris Basin: Potential for energy production from organic-rich shales – Margaux Meslé – International Journal of Coal Geology

All ecosystems potentially host electrogenic bacteria – Nicolas Chabert – Bioelectrochemistry

Phylogenetic structure of arbuscular mycorrhizal community shifts in response to increasing soil fertility – Yongjun Liu – Soil Biology and Biochemistry

Water and extremophile microbiome

Phytoplankton–bacterial interactions mediate micronutrient colimitation at the coastal Antarctic sea ice edge – Erin M. Bertrand – PNAS

Effects of hydrostatic pressure on yeasts isolated from deep-sea hydrothermal vents – Gaëtan Burgaud- Research in Microbiology

Identification of Habitat-Specific Biomes of Aquatic Fungal Communities Using a Comprehensive Nearly Full-Length 18S rRNA Dataset Enriched with Contextual Data – Katrin Panzer – PLOS ONE

Metaproteomics of aquatic microbial communities in a deep and stratified estuary – David Colatriano – Proteomics

Waste treatment microbiology

Review: Meta-omics approaches to understand and improve wastewater treatment systems – Elisa Rodríguez – Reviews in Environmental Science and Bio/Technology

Metagenomics and bioinformatics

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples – Tal Korem – Science

Spaced seeds improve k-mer-based metagenomic classification – Karel Břinda – Bioinformatics

Microbial Ecology

Resource pulses can alleviate the biodiversity–invasion relationship in soil microbial communities – Cyrus A. Mallon – Ecology

Not sure if I like this term: Tritagonist as a new term for uncharacterised microorganisms in environmental systems – Florian M Freimoser – ISME Journal

Microbes in the news

Bacteria on chicken, turkey, pork linked to bladder infections – Lynne Terry – Oregon Live

Byproduct of intestinal bacteria may jeopardize heart health in kidney disease patients – Medical Xpress

Oregon architecture researchers to study indoor air quality in 72 homes – EurekAlert

Research spotlights a previously unknown microbial ‘drama’ playing in the Southern Ocean – Science Daily

Government of Canada Invests in New Western Canadian Microbiome Centre – Sys-Con Media

A Video of the destruction can be seen here: Wood-Decay Fungus Identified as Culprit Consuming Pomona Family’s Home – LA Testing

Microbes and Art

Don’t Be Grossed Out, The Bacteria On These Petri Dish Plates Is Art – Andrew Liszewski – Gizmodo

Call for Entries! ASM’s 2015 Agar Art Contest: Submit your work by September 3th – MicrobeWorld

Bik’s Picks: drought edition

Puget Sound sweltering from the drought and Blob – Department of Ecology – Courier Herald

Extreme Droughts Weaken Trees’ Ability to Soak Up Carbon – William R L Anderegg – Gizmodo

It’s Raining Spiders! Weirdest Effects of California Drought – Tia Ghose – Live Science

[hr]

July 25, 2015

Posted on by

Extracting DNA from the soil under a cadaver, metabolomics of periodontitis, HLA haplotypes and microbiome, and microbes using ancient carbon from melting permafrost.

Microbiome of pregnancy and health

Gut Bifidobacterium microbiota in one-month-old Brazilian newborns – Łukasz Grześkowiak – Anaerobe

Microbiome of death

Assessment of microbial DNA extraction methods of cadaver soil samples for criminal investigations – Sheree J. Finley – Australian Journal of Forensic Sciences

Human oral microbiome

Editorial: Targeting specific bacteria in the oral microbiome – Jorge Frias-Lopez – Trends in Microbiology

The human salivary microbiome exhibits temporal stability in bacterial diversity – Simon J. S. Cameron – FEMS Microbiology Ecology

Association of Synergistetes and Cyclodipeptides with Periodontitis – J.T. Marchesan – Journal of Dental Research

Human urinary tract microbiome

Article in Russian: Microbial communities on kidney stones – YM Romanova – Mol Gen Mikrobiol Virusol

Human gut microbiome

The Influence of the Autoimmunity-Associated Ancestral HLA Haplotype AH8.1 on the Human Gut Microbiota: A Cross-Sectional Study – Johannes R. Hov – PLOS ONE

Clostridium amazonense sp. nov. an obliqately anaerobic bacterium isolated from a remote Amazonian community in Peru – Lindsey O’Neal – Anaerobe

Crohn-associated microbial communities from colonic mucosal biopsies in patients of the western Mediterranean – Roberto Vidal – Systematic and Applied Microbiology

Human eye microbiome

Bacteria Colonizing the Ocular Surface in Eyes With Boston Type 1 Keratoprosthesis: Analysis of Biofilm-Forming Capability and Vancomycin Tolerance – Sarmad H. Jassim – Investigative Ophthalmology & Visual Science

Microbiome models

Persistent hyperglycemia modulates gut immune function and microbiota in rats – Katsuya Mori – Journal of Intensive Care

Animal microbiome

16S rDNA analysis of archaea indicates dominance of Methanobacterium and high abundance of Methanomassiliicoccaceae in rumen of Nili-Ravi buffalo – S.S. Paul – Anaerobe

Developmental succession of the microbiome of Culex mosquitoes – Dagne Duguma – BMC Microbiology

Plant, root, and soil microbiome

Fungal colonization of the rooting system of the early land plant Asteroxylon mackiei from the 407-Myr-old Rhynie Chert (Scotland, UK)- Christine Strullu-Derrien – Botanical Journal of the Linnean Society

Soils, microbes, and forest health: A qualitative analysis of social and institutional factors affecting genomic technology adoption – Sara E. Crann – Technology in Society

Assessment of microbial DNA extraction methods of cadaver soil samples for criminal investigations – Sheree J. Finley – Australian Journal of Forensic Sciences

Water microbiome

Spatial patterns of benthic bacterial communities in a large lake – Li-Xiang Liu – International Review of Hydrobiology

Extremophile microbiome

Utilization of ancient permafrost carbon in headwaters of Arctic fluvial networks – Paul J. Mann – Nature Communications

Waste water and bioreactor microbiology

Determination of the archaeal and bacterial communities in two-phase and single-stage anaerobic systems by 454 pyrosequencing – Yogananda Maspolim – Journal of Environmental Sciences

Influence of co-substrate on textile wastewater treatment and microbial community changes in the anaerobic biological sulfate reduction process – Kashif Rasool – Journal of Hazardous Materials

Metabolic networks

Metabolic interactions in microbial communities: untangling the Gordian knot – Olga Ponomarova – Current Opinion in Microbiology

Association of Synergistetes and Cyclodipeptides with Periodontitis – J.T. Marchesan – Journal of Dental Research

Microbes in the news

If the sea is dirty, the sand is worse. Beach sand contains more fecal bacteria than seawater – Megan Scudellari – Boston Globe

Bacteria Hysteria

The Best Way To Clean Your Purse From All That Dirty Bacteria – Madelyn Chung – Huffington Post Canada

Breast milk containing bacteria for sale on Craigslist in Upstate – Gabrielle Komorowski – WYFF4

Bik’s Picks

What San Diego Scientists Are Discovering About Dolphins And Diabetes – Megan Burke – KPBS

Bid to save dolphins in polluted Ganges – Nirmala Ganapathy – Straits Times

 

The SnotBot: Patrick Stewart Backs Drones That Collect Whale Snot – Keith Wagstaff – NBC News

[hr]

July 24, 2015

Posted on by

A review about small molecules produced by human microbiota, layers of microbial life in Dead Sea sediments, fungus making “hair ice”, exploring deep microbial life in the sea, and bacterial diversity at the North Pole.

Events

3rd Microbiome R&D and Business Collaboration Forum: USA, San Diego, September 10-11, 2015

WAO Symposium on Food Allergy & the Microbiome – 5-6 December 2015, Miami, FL

Microbiome reviews

Small molecules from the human microbiota – Mohamed S. Donia, Michael A. Fischbach – Science

Editorial: Microbiota-induced T cells block allergic inflammation – Yvonne Bordon – Nature Reviews Immunology

Perspective: Promise and pragmatism in clinical microbiome research – Nadim J. Ajami – Mini-Reviews in Medicinal Chemistry

Review: The Role of Intestinal Microbiota in Graft versus Host Disease – no authors listed – Mini-Reviews in Medicinal Chemistry

Editorial: Protective role of gut microbial SCFAs – Ellen F. Carney – Nature Reviews Nephrology

Human oral microbiome

In vitro work: Low-dose irradiation affects the functional behavior of oral microbiota in the context of mucositis – Barbara WA Vanhoecke – Experimental Biology and Medicine

Human gut microbiome

Agave Inulin Supplementation Affects the Fecal Microbiota of Healthy Adults Participating in a Randomized, Double-Blind, Placebo-Controlled, Crossover Trial – Hannah D Holscher – Journal of Nutrition

Plant, root, and soil microbiome

Impact of paleoclimate on the distribution of microbial communities in the subsurface sediment of the Dead Sea – C. Thomas – Geobiology

Evidence for biological shaping of hair ice – D. Hofmann – Biogeosciences

Water and extremophile microbiome

Exploring deep microbial life in coal-bearing sediment down to ~2.5 km below the ocean floor – F. Inagaki – Science

Morphological and phylogenetic diversity of thermophilic cyanobacteria in Algerian hot springs – Samia Amarouche-Yala – Extremophiles

Bacterial diversity in snow on North Pole ice floes – Aviaja L. Hauptmann – Extremophiles

Identifying the sources of nitrate contamination of groundwater in an agricultural area (Haean basin, Korea) using isotope and microbial community analyses – Heejung Kim – Science of the Total Environment

Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages – Haiwei Luo – Molecular Biology and Evolution

Built environment microbiome

Microbiological characterization of 3193 French dwellings of Elfe cohort children – S. Rocchi – Science of The Total Environment

Metagenomics and bioinformatics

For plant/animal assemblages, but might be of interest: cati: an R package using functional traits to detect and quantify multi-level community assembly processes – Adrien Taudiere – Ecography

Metabolomics and proteomics

Metaproteomics and metabolomics analyses of chronically petroleum-polluted sites reveal the importance of general anaerobic processes uncoupled with degradation – Rafael Bargiela – Proteomics

Microbes in the news

‘It’s like going to Pluto and seeing McDonald’s: ‘These microbes live more than 2 kilometers below the sea floor off the coast of Japan – Mitch Leslie – Science

It takes a village… to ward off dangerous infections? New microbiome research suggests so – MedicalXpress

Pathogenic microbiome bacteria change shape to adapt to nasopharyngeal environment – American Microbiome Institute

Rotting Fungus Creates Beautiful, Glistening ‘Hair Ice’ – Elizabeth Goldbaum – LiveScience

Not endorsing this one, full of errors and false claims: Discovery of Microbiome “Third Brain” Confirmed by Scientific Research in Japan – BusinessWire

Science, publishing, and career

New life for old bones: inventing ways to apply the DNA sequencing revolution to tissues ravaged by time. – Elizabeth Culotta – Science

Songwriting and science: Pitching songs, however, has taught me a few practical lessons about pitching papers and grant proposals: – C. Neal Stewart Jr. – Science

Bik’s Picks

Comparisons of life-history parameters between free-ranging and captive killer whale (Orcinus orca) populations for application toward species management – Todd R. Robeck – Journal of Mammalogy

Kiwi genome provides insights into evolution of a nocturnal lifestyle – Diana Le Duc – Genome Biology

A medical-toxicological view of tattooing – Peter Laux – The Lancet

[hr]