Category Archives: Techniques

November 12, 2015

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Gut microbiome and definition of self, symbionts of corals and algae, and microbial geobiology of space exploration. And – yeah! – my Twitter account made it to a “Top 100 Twitter Influencers Working in Life Sciences” list. My Twitter handle is @MicrobiomDigest.

Human gut microbiome

Extensive T-cell epitope repertoire sharing among human proteome, gastrointestinal microbiome, and pathogenic bacteria: implications for the definition of self –
Robert D. Bremel – Frontiers in Immunology

Gut microbiota and diet in patients with different glucose tolerance – Lilit Vanikovna Egshatyan – Endocrine Connections

Review: Alcoholic Liver Disease: The Gut Microbiome and Liver Cross Talk – Phillipp Hartmann – Alcoholism: Clinical and Experimental Research

Review: Linking Microbiota to Human Diseases: A Systems Biology Perspective – Hao Wu – Trends in Endocrinology & Metabolism

Review: Gut microbiota and host metabolism in liver cirrhosis – Makoto Usami – World Journal of Gastroenterology

Infection and cancer microbiology

Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis – Samuel A. Shelburne – PLOS ONE

Animal microbiome

Open Access: Stable and sporadic symbiotic communities of coral and algal holobionts – Eric R. Hester – The ISME Journal

Plant, root, and soil biology

Past water management affected GHG production and microbial community pattern in Italian rice paddy soils – A. Lagomarsino – Soil Biology and Biochemistry

Elemental stoichiometry indicates predominant influence of potassium and phosphorus limitation on arbuscular mycorrhizal symbiosis in acidic soil at high altitude –
Mohammad Haneef Khan – Journal of Plant Physiology

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach – P. Bhattacharyya – Science of The Total Environment

Food microbiology

Monitoring of spoilage and determination of microbial communities based on 16S rRNA gene sequence analysis of whole sea bream stored at various temperatures – Foteini F. Parlapani – LWT – Food Science and Technology

Variation in fungal microbiome (mycobiome) and aflatoxin in stored in-shell peanuts at four different areas of China – Ning Ding – Frontiers in Microbiology

Waste microbiology

Characterization of successional changes in bacterial community composition during bioremediation of used motor oil-contaminated soil in a boreal climate – Lijuan Yan – Science of the Total Environment

Space microbiology

An ESA Roadmap for Geobiology in Space Exploration – Claire R Cousins – Acta Astronautica

Transcriptomics

Protocol: Prokaryotic Metatranscriptomics – Danilo Pérez-Pantoja – Springer Protocols Handbooks

Microbes in the news

Story behind the paper: Porphyrobacter mercurialis, a new species found by #citizenscience and then sent to the #iss – David Coil – MicroBEnet

Getting a flu shot every year? More may not be better – Helen Branswell – STAT news

Dangerous liaison: Bacteria, viruses in league – Bruce Goldman – Stanford Medicine News

Filamentous Bacteriophage Promote Biofilm Assembly and Function – Patrick R. Secor – Cell Host & Microbe

Intestinal Pathogens Change the Microbiome, Cause E. Coli To “Bloom” – Interview with Shannon D. Manning – Medical Research

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November 10, 2015

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Oral and gut microbiomes respond differently to antibiotics, looking two gifted horses in the mouth, BMIs and Bifidos, Drosophila mating, gut microbes and tumorigenesis, microbial food webs in clay rocks, and don’t forget that Bonferroni correction.

Pregnancy and birth (Probiotics too!)

Endometrial microbiome at the time of embryo transfer: next-generation sequencing of the 16S ribosomal subunit – J. M. Franasiak – Journal of Assisted Reproduction and Genetics

Association of Early Exposure of Probiotics and Islet Autoimmunity in the TEDDY Study – Ulla Uusitalo – JAMA Pediatrics

Human oral microbiome

Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces – Egija Zaura – mBio

Crossover clinical trial of different methods of removing a denture adhesive and the influence on the oral microbiota – Élen Massaro Nunes – The Journal of Prosthetic Dentistry

Human gut microbiome

Correlation between body mass index and fecal microbiota from children – A. Ignacio – Clinical Microbiology and Infection

Review: Clostridium difficile infection and intestinal microbiota interactions – C. Rodriguez – Microbial Pathogenesis

Animal and bioreactor models

A Statistical Error in: “Analysis of Caecal Microbiota in Rats Fed with Genetically Modified Rice by Real-Time Quantitative PCR” – Alexander Panchin – Journal of Food Science

In mice: Manipulation of the Gut Microbiota Reveals Role in Colon Tumorigenesis -Joseph P. Zackular – mSphere

The impacts of Wolbachia and the microbiome on mate choice in Drosophila melanogaster – Devin Arbuthnott – Journal of Evolutionary Biology

Chemostat culture systems support diverse bacteriophage communities from human feces – Tasha M. Santiago-Rodriguez – Microbiome

Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans – Nicholas A. Pudlo – mBio

Temporal dynamics of the metabolically active rumen bacteria colonising fresh perennial ryegrass – Sharon A. Huws – FEMS Microbiology Ecology

Animal microbiome

In-depth snapshot of the equine subgingival microbiome – Wenling Gao – Microbial Pathogenesis

Occurrence and distribution of Malassezia species on skin and external ear canal of horses – Hojjatollah Shokr – Mycoses

Review: The functionality of the gastrointestinal microbiome in non-human animals – Irene Hanning – Microbiome

Plant, root, and soil microbiome

The effect of altitudinal gradient on soil microbial community activity and structure in moso bamboo plantations – Ed-Haun Chang – Applied Soil Ecology

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities – Stephane Uroz – Trends in Microbiology

Soil and Rhizosphere Associated Fungi in Grey Mangroves (Avicennia marina) from the Red Sea – A Metagenomic Approach – Marta Filipa Simões – Genomics, Proteomics & Bioinformatics

Deciphering Community Structure of Methanotrophs Dwelling in Rice Rhizospheres of an Indian Rice Field Using Cultivation and Cultivation-Independent Approaches – Pranitha S. Pandit – Environmental Microbiology

Effects of Sulfamethazine and Zinc on the Functional Diversity of Microbial Communities during Composting – Manli Duan – Environmental Microbiology

Evidence for duplication in title words: Prokaryotes in subsoil – evidence for spatial separation of oligotrophs and copiotrophs by co-occurrence networks – Michael Schloter – Frontiers in Microbiology

A minimalistic microbial food web in an excavated deep subsurface clay rock -Alexandre Bagnoud – FEMS Microbial Ecology

Water microbiome

Chemical dispersants can suppress the activity of natural oil-degrading microorganisms – Sara Kleindienst – PNAS

Extremophile microbiome

Distribution and diversity of microbial communities in meromictic soda Lake Doroninskoe (Transbaikalia, Russia) during winter – Evgeniya Matyugina – Chinese Journal of Oceanology and Limnology

Built environment microbiome

Differences in intertidal microbial assemblages on urban structures and natural rocky reef – Elisa L. Tan – Frontiers in Microbiology

Waste microbiology

Diverse Bacterial Groups Contribute to the Alkane Degradation Potential of Chronically Polluted Subantarctic Coastal Sediments – Lilian M. Guibert – Environmental Microbiology

Cultivating Microbial Dark Matter in Benzene-Degrading Methanogenic Consortia –
Fei Luo – Environmental Microbiology

Metagenomics and bioinformatics

DESM: portal for microbial knowledge exploration systems – Adil Salhi – Nucleic Acids Research

Techniques

Coupling dye-integrated polymeric membranes with smartphone detection to classify bacteria – Lígia Bueno – RSC Advances

Microbes in the news

9 Fascinating Facts About The Microbiome, The Trillions Of Microbes Hidden Inside Us — Jessica Leber – Fast Co.Exist

NTU scientists use dead bacteria to kill colorectal cancer – EurekAlert

Science, publishing, and career

(A)Historical Science: why scientists should care more about the history of science – Arturo Casadevall and Ferric C. Fang – Infection and Immunity

November 9, 2015

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Bronchial microbiome in COPD patients, tilapia pond systems, bacteria and fungi at the root tips of Pinus, and microbiome of an extreme Australian river.

Human respiratory microbiome

Influence of biofim on the bronchial microbiome in COPD patients colonized or infected by pseudomonas aeruginosa – Marian Garcia-Nuñez – European Respiratory Journal

Human gut microbiome

Review: Gut Microbiota and Host Reaction in Liver Diseases – Hiroshi Fukui – Microorganisms

Animal models

Repeated dose (28-day) administration of silver nanoparticles of varied size and coating does not significantly alter the indigenous murine gut microbiome – Laura A. Wilding – Nanotoxicology

Animal microbiome

Bacteria associated with Amblyomma cajennense tick eggs – Erik Machado-Ferreira – Genetics and Molecular Biology

Characterization of microbial communities in intensive GIFT tilapia (Oreochromis niloticus) pond systems during the peak period of breeding – Limin Fan – Aquaculture Research

Plant, root, and soil microbiome

Novel mycoviruses discovered from metatranscriptomics survey of soybean phyllosphere phytobiomes – Shin-Yi Lee Marzano – Virus Research

The local environment determines the assembly of root endophytic fungi at a continental scale – Kyriaki Glynou – Environmental Microbiology

Effects of vegetation and seasonality on bacterial communities in Amazonian dark earth and adjacent soils – Amanda Barbosa Lima – African Journal of Microbiology Research

Response of soil microbiota to nine-year application of swine manure and urea – Diana Morales – Ciencia Rural

Analysis of single root-tip microbiomes suggests that distinctive bacterial communities are selected by Pinus sylvestris roots colonized by different ectomycorrhizal fungi – Srisailam Marupakula – Environmental Microbiology

The structure of microbial community in aggregates of a typical chernozem aggregates under contrasting variants of its agricultural use – E. A. Ivanova – Soil Biology

Water management impacts on arsenic behavior and rhizosphere bacterial communities and activities in a rice agro-ecosystem – Suvendu Das – Science of The Total Environment

Functional selections of soil metagenomes identify tolerance genes against lignocellulose-derived inhibitors – Kevin J. Forsberg – Applied and Environmental Microbiology

Characterization of the core microbiota of the drainage and surrounding soil of a Brazilian copper mine – Letícia Bianca Pereira – Genetics and Molecular Biology
http://www.scielo.br/scielo.php?pid=S1415-47572015005050025&script=sci_arttext
Water / Extremophile microbiome

Extremophile microbiomes in acidic and hypersaline river sediments of Western Australia – Shipeng Lu – Environmental Microbiology Reports

Food microbiology

Impact of nisin-activated packaging on microbiota of beef burgers during storage – Ilario Ferrocino – Applied and Environmental Microbiology

Techniques

PacBio Sequencing and Its Applications – Anthony Rhoads – Genomics, Proteomics & Bioinformatics

Preservation of Uncultivated Microbial Cells for Single Cell Genomics and Cultivation in Future – Om Prakash – Single Cell Biology

Microbes in the news

Kangaroo farts won’t save the world – Their gut microbes really aren’t that special – Arielle Duhaime-Ross

Based on the data shown here, the title seems a stretch: 2015 American College of Rheumatology Annual Meeting: Microbiome Seems to Have a Role in Triggering Lupus – HCP Live

Bacteria looks to be promising in cheatgrass battle – Larry Meyer – The Argus Observer
http://www.argusobserver.com/news/bacteria-looks-to-be-promising-in-cheatgrass-

Veterinarians Warn Pet Owners About Bacteria After Flooding: increased chance of leptospirosis – TWC news
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November 4, 2015

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Lots of upcoming workshops and seminars, genome-wide association of the human gut microbiota, contamination of cord blood units, and bacteria with the rRNA genes on a plasmid, not on their chromosome.

Events

Webinar: The ageing microbiota by Gemma Walton and Annie-Rose Harrison-Dunn – November 17, 2015 – 10AM Paris

Mothur 3-day workshop organized by Pat Schloss – December 16-18, Detroit.

2nd Microbiome R&D and Business Collaboration Congress: Asia – February 29-March 1 2016, Kuala Lumpur, Malaysia

Early career workshop on Microbiology of the built environment (Chicago, IL) – Jack Gilbert lab – April 26-29 2016

Human oral microbiome

Pyrosequencing of Plaque Microflora In Twin Children with Discordant Caries Phenotypes – Meng Zhang – PLOS ONE

Human gut microbiome

In Hutterites: Genome-Wide Association Studies of the Human Gut Microbiota – Emily R. Davenport – PLOS ONE

Lactobacillus casei Shirota Supplementation Does Not Restore Gut Microbiota Composition and Gut Barrier in Metabolic Syndrome: A Randomized Pilot Study – Vanessa Stadlbauer – PLOS ONE

Infection microbiology

Microbial Contaminants of Cord Blood Units Identified by 16S rRNA Sequencing and by API Test System, and Antibiotic Sensitivity Profiling – Luís França – PLOS ONE

More microbes

Bacterial clade with the ribosomal RNA operon on a small plasmid rather than the chromosome – Mizue Anda – PNAS

High-throughput 3D tracking of bacteria on a standard phase contrast microscope –
K.M. Taute – Nature Communications

Automated image analysis for quantification of filamentous bacteria – Marlene Fredborg – BMC Microbiology

Microbial ecology

Community rescue in experimental metacommunities – Etienne Low-Décarie – PNAS

Microbes in the news

Family dog lowers kids’ asthma risk, proving dirt and bacteria are good for children – Shelley Hazen – Inquisitr

Microbiome expert Martin Blaser to receive Georgetown’s Cura Personalis Award Nov. 3 – EurekAlert

Microbiomes could prove essential in various fields of science, study suggests – Kimberly Nielsen – The Daily Californian

Salivary microbiome of whitetail deer: Mature doe set the rut timetable – Oak Duke – Wellsville Daily Reporter

Finally! New germ exhibit opening at the American Museum of Natural History – Rebecca Rosenthal – North Jersey

Thank heavens, someone figured out which bacteria live on a donkey’s penis – Discover
http://blogs.discovermagazine.com/seriouslyscience/2015/11/03/thank-heavens-

How was the bacteria at York Hospital found?– Dylan Segelbaum – York Daily Record

Worms (and germs) may be the answer to preventing allergies – Jason Tetro – Popular Science

Two Million-Year-Old Bacteria Used Iron “Sunscreen” – Charlotte Ward – RedBrick

Bacteria infecting orange groves is driving up cost of juice; threatens nation’s supply – Sandy Miller – Fox2Now

Science, publishing, and career

EU urges science publishers to adapt to open access: European research commissioner Carlos Moedas has urged journal publishing companies to reshape their business models to an open access system. – LabNews

Supervision: Clear direction: Managing laboratory members as well as a research strategy can be difficult for early-career principal investigators, but help is at hand. – Boer Deng – Nature

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November 3, 2015

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Dog exposure and childhood asthma, earthworm poop, thermally stressed corals, and cryospheric ecosystems.

General microbiome

From culturomics to taxonomogenomics: A need to change the taxonomy of prokaryotes in clinical microbiology – Pierre-Edouard Fournier – Anaerobe

Study from Sweden with patients and dogs registries: Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma – Tove Fall – JAMA Pediatrics

Human gut microbiome

Plagiarism in intro and only CFU data for E. coli and lactic acid bacteria: A Comparative Study of Gut Microbiota Profiles of Children Living in Kulon Progo and West Lombok – Siti Helmyati – Pakistan Journal of Nutrition

Microbial Signatures in Post-Infectious Irritable Bowel Syndrome – Towards Patient Stratification for Improved Diagnostics and Treatment – Jonna Jalanka – Gut Microbes

Review: Genetic Variations in Vitamin D Metabolism Genes and the Microbiome, in the Presence of Adverse Environmental Changes, Increase Immune Dysregulation – Laing BB
and Ferguson LR – Austin Journal of Nutrition & Metabolism

Animal models

In mice: Gut microbe-derived extracellular vesicles induce insulin resistance, thereby impairing glucose metabolism in skeletal muscle – Youngwoo Choi – Scientific Reports

In mice: Influence of whole-wheat consumption on fecal microbial ecology of obese diabetic mice – Jose F Garcia-Mazcorro – PeerJ Preprints

Earthworms: Characterization of the bacterial communities of casts from Eisenia andrei fed with different substrates – Manuel Aira – Applied Soil Ecology

Animals

Viral and Bacterial Epibionts in Thermally-Stressed Corals – Hanh Nguyen-Kim – J Mar Sci Eng

Plant, root, and soil microbiome

Cross-biome comparison of microbial association networks – Karoline Faust – Frontiers in Microbiology

Response of microbial communities from an apple orchard and grassland soils to the first-time application of the fungicide tetraconazole – Sławomir Sułowicz – Ecotoxicology and Environmental Safety

A Chemical Perspective on Microalgal–Microbial Interactions – Erik F.Y. Hom – Trends in Plant Science

Availability of different nitrogen forms changes the microbial communities and enzyme activities in the rhizosphere of maize lines with different nitrogen use efficiency – Laura Giagnoni – Applied Soil Ecology

Shifts in microbial communities do not explain the response of grassland ecosystem function to plant functional composition and rainfall change – Ellen L. Fry – Soil Biology and Biochemistry

Copper and temperature modify microbial communities, ammonium and sulfate release in soil – Rui Ferreira – Journal of Plant Nutrition and Soil Science

Review: Mitigating climate change through managing constructed-microbial communities in agriculture – Cyd E. Hamilton – Agriculture, Ecosystems & Environment

Extremophile microbiome

Editorial: Cryospheric ecosystems: a synthesis of snowpack and glacial research – Andy Hodson – Environmental Research Letters

Bioinformatics and metagenomics

AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities – Anja Lange – PLOS ONE

Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes – Mingjie Wang – Genome Biology

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets – Yu-Wei Wu – Bioinformatics

Techniques

Integrated micro-optofluidic platform for real-time detection of airborne microorganisms – Jeongan Choi – Scientific Reports

Microbes in the news

Microbesity: Obesity appears linked to the gut microbiome. How and why is still a mystery—but scientists have plenty of ideas – Jenny Rood – The Scientist

Science, publishing, and career

“There’s No Crying in Academia,” Acknowledging Emotional Labour in the Academy  – Margeaux Feldman – Gender and Society

2015 Life Sciences Salary Survey – Karen Zusi and Amanda B. Keener – The Scientist
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October 29, 2015

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Library prep technology, skin communities in urban and rural populations, rarity in aquatic microbes, and the microbiome of solar panels.

Pregnancy and birth

The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons – Anuradha Ravi – Scientific Reports

Associations between human milk oligosaccharides and infant body composition in the first 6 mo of life – Tanya L Alderete – The American Journal of Clinical Nutrition

Human skin microbiome

The Influence of Age and Gender on Skin-Associated Microbial Communities in Urban and Rural Human Populations – Shi Ying – PLOS ONE

Human respiratory microbiome

Review: A comprehensive review of the nasal microbiome in chronic rhinosinusitis (CRS) – Mahboobeh Mahdavinia – Clinical & Experimental Allergy

Human gut microbiome

Lactobacillus casei Shirota Supplementation Does Not Restore Gut Microbiota Composition and Gut Barrier in Metabolic Syndrome: A Randomized Pilot Study – Vanessa Stadlbauer – PLOS ONE

DGGE: The duodenal microbiota composition in children with active coeliac disease is influenced for the degree of enteropathy – F. Girón Fernández-Crehuet – Anales de Pediatría (English Edition)

Review: The microbiome and its pharmacological targets: therapeutic avenues in cardiometabolic diseases – Ana Luisa Neves – Current Opinion in Pharmacology

Review: Microbiome impact on metabolism and function of sex, thyroid,
growth and parathyroid hormones – Michał Kunc – Acta Biochimica Polonica

Review: Intestinal Microbiota: From Inflammatory Bowel Disease to Bone Marrow Transplantation – Ernst Holler – Blood

Review: Dysbiotic gut microbiome: A key element of Crohn’s disease – Styrk Furnes Øyri – Comparative Immunology, Microbiology and Infectious Diseases

Infection microbiology

Serum bacterial DNA detection in patients with cholangitis after Kasai procedure – Qianfu Luo – Pediatrics International

Deceiving title (not about microbiome but infection): Breast Implant–Associated Infections: The Role of the National Surgical Quality Improvement Program and the Local Microbiome – Cohen, Justin B. – Plastic and Reconstructive Surgery

Influence of microbiome species in hard-to-heal wounds on disease severity and treatment duration – Dagmar Chudobova – The Brazilian Journal of Infectious Diseases

Animal and bioreactor models

The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia – Tim J Schuijt – Gut

In mice: The Intestinal Microbiota Contributes to the Ability of Helminths to Modulate Allergic Inflammation – Mario M. Zaiss – Cell

Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization – Malin E.V. Johansson – Cell Host & Microbe

Microbiota-Dependent Hepatic Lipogenesis Mediated by Stearoyl CoA Desaturase 1 (SCD1) Promotes Metabolic Syndrome in TLR5-Deficient Mice – Vishal Singh – Cell Metabolism

Influences of graphene on microbial community and antibiotic resistance genes in mouse gut as determined by high-throughput sequencing – Yongchao Xie – Chemosphere

The longitudinal effect of a multi-strain probiotic on the intestinal bacterial microbiota of neonatal foals – A. Schoster – Equine Veterinary Journal

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

Assessment of prebiotic potential of Akpan-yoghurt-like product and effects on the human intestinal microbiota – Beatriz Gullón – Journal of Functional Foods

Relationship between inflammation, the gut microbiota, and metabolic osteoarthritis development: studies in a rat model – K.H. Collins – Osteoarthritis and Cartilage

Plant, root, and soil microbiome

Long-term reactive nitrogen loading alters soil carbon and microbial community properties in a subalpine forest ecosystem – Claudia M. Boot – Soil Biology and Biochemistry

Do arbuscular mycorrhizal fungi stabilize litter-derived carbon in soil? – Erik Verbruggen – Journal of Ecology

Editorial: Does Microbial Diversity Confound General Predictions? – Marie Duhamel – Trends in Plant Science

Water microbiome

Review: Rarity in aquatic microbes: placing protists on the map – Ramiro Logares – Research in Microbiology

Waste microbiology

Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion – Eoin Gunnigle – FEMS Microbiology Ecology

An ‘omics’ approach towards the characterisation of laboratory scale anaerobic digesters treating municipal sewage sludge – D.J. Beale – Water Research

Extremophile microbiome

Functional analysis of the archaea, bacteria, and viruses from a halite endolithic microbial community – Alexander Crits-Christoph – BioRxiv

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city – Pedro Dorado-Morales – BioRxiv

Food microbiology

Microbial community dynamics in thermophilic undefined milk starter cultures – Eugenio Parente – International Journal of Food Microbiology

Metagenomics and bioinformatics

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition – David Koslicki – PLOS ONE

Linear-time superbubble identification algorithm for genome assembly – Ljiljana Brankovic – Theoretical Computer Science

Bifidobacteria exhibit social behavior through carbohydrate resource sharing in the gut – Christian Milani – Scientific Reports

Power law analysis of the human microbiome – Zhanshan (Sam) Ma – Molecular Ecology

More microbiology

Bioactive natural products from novel microbial sources – Victoria L. Challinor – Annals of the New York Academy of Sciences

Conference report: Bacterial Networks in Cells and Communities – Victor Sourjik – Journal of Molecular Biology

Self-establishing communities enable cooperative metabolite exchange in a eukaryote – Kate Campbell – eLife

Techniques

Library preparation methodology can influence genomic and functional predictions in human microbiome research – Marcus B. Jones – PNAS

Microbes in the news

Scientists Urge National Initiative on Microbiomes – Carl Zimmer – New York Times

Fecal transplant pills: Large-scale production begins: Nonprofit stool bank launched by MIT researchers completes first dose-finding study – GlobeNewsWire
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October 15, 2015

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Upcoming Reddit AMA with Jessica Richman, oral microbiome transplants, meta-analysis of the indoor environment, African gut microbiota, corals, lichens, and more.

Events

Ask Me Anything (AMA) with Jessica Richman from uBiome on Reddit. October 16 from 10-11am PT

Human oral microbiome

Towards microbiome transplant as a therapy for periodontitis: an exploratory study of periodontitis microbial signature contrasted by oral health, caries and edentulism – Alex E. Pozhitkov – BMC Oral Health

Human gut microbiome

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease – James D. Lewis – Cell Host & Microbe

Variation in rural African gut microbiota is strongly correlated with colonization by Entamoeba and subsistence – Elise R Morton – BioRxiv

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

Animal models

Analysis of Bacterial Communities during Clostridium difficile Infection in the Mouse – Ekaterina G. Semenyuk – Infection and Immunity

Structural & Functional Consequences of Chronic Psychosocial Stress on the Microbiome & Host – Aadil Bharwani – Psychoneuroendocrinology

Animal microbiome

Pyrosequencing of the bacteria associated with Platygyra carnosus corals with skeletal growth anomalies reveals differences in bacterial community composition in apparently healthy and diseased tissues – Jenny C. Ng – Frontiers in Microbiology

Plant, root, and soil microbiome

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

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

Fungal Biodiversity in the Alpine Tarfala Valley – Claudia Coleine – Microorganisms

Effects of long-term drainage on microbial community composition vary between peatland types – Zuzana Urbanová – Soil Biology and Biochemistry

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

Soil organic matter quantity and quality shape microbial community compositions of subtropical broadleaved forests – Junjun Ding – Molecular Biology

Built environment microbiome

Microbiota of the indoor environment: a meta-analysis – Rachel I. Adams – Microbiome

Microbial ecology

Private benefits and metabolic conflicts shape the emergence of microbial interdependencies – Sylvie Estrela – Environmental Microbiology

Techniques

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples – Alma E. Parada – Environmental Microbiology

Microbes in the news

Metagenomics Digs Up Microbiome Riches: Researchers Are Consulting Metagenomic Maps and Equipping Themselves with Computational Models and Analytical Tools – GenEnNews

Differences in treatment effect on out-of-balance microbiome in Crohn’s disease – EurekAlert

Pets and Owners May Share MRSA Bacteria – Rachael Rettner – LiveScience

Cultural Riches: Researchers devise new techniques to facilitate growing bacteria collected from the environment – Anna Azvolinsky – The Scientist

This could be our best defense against the antibiotic apocalypse: Carl Zimmer on phage therapy – Lydia Ramsey – Business Insider

Bacteria Hysteria

Millions of mattresses are swarming with bacteria and mould that ‘trigger skin infections, asthma and allergies’ – Fiona Macrae – Daily Mail

Microbiology and art

These Photos Reveal How Magnificent Our World Is On The Micro Level: The award-winning images represent some of the best microphotography from around the world – Jacqueline Howard – Huffington Post

How Lining Yao adapted bacteria into living clothing and biomaterials – Matt Kamen – Wired

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October 10, 2015

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The Eukaryome of the human gut, core microbiome in rumen, overweight kitties, and viral metagenomics of a hot spring.

Human gut microbiome

Repertory of Eukaryotes (Eukaryome) in the Human Gastrointestinal Tract: Taxonomy and Detection Methods – Ibrahim Hamad – Parasite Immunology

Diversity of Duodenal and Rectal Microbiota in Biopsy Tissues and Luminal Contents in Healthy Volunteers – Gangping Li – Journal of Microbiology and Biotechnology

Role of the Gut Microbiome in Nonalcoholic Fatty Liver Disease – Bashar Aqel, John K. DiBaise – Nutrition in Clinical Practice

Review: Gut Microbiome: What We Do and Don’t Know – Gail A. Cresci and Emmy Bawden – Nutrition in Clinical Practice

Editorial: Contribution of Gut Bacteria to Lipid Levels Another Metabolic Role for Microbes? – Hooman Allayee, Stanley L. Hazen

Human vaginal microbiome

Enhanced Trapping of HIV-1 by Human Cervicovaginal Mucus Is Associated with Lactobacillus crispatus-Dominant Microbiota – Kenetta L. Nunn – mBio

Models of microbiome research

Microbiota-Dependent Sequelae of Acute Infection Compromise Tissue-Specific Immunity
Denise Morais da Fonseca – Cell

Animal microbiome

Overweight and the feline gut microbiome – a pilot study – I. N. Kieler – Journal of Animal Physiology and Animal Nutrition

Bovine mastitis may be associated with the deprivation of gut Lactobacillus – C. Ma – Beneficial Microbes

Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range – Gemma Henderson – Scientific Reports

Plant, root, and soil microbiome

Evaluating a multigene environmental DNA approach for biodiversity assessment
Alexei J. Drummond – GigaScience (via PMC)

Sheep grazing and soil bacterial diversity in shrublands of the Patagonian Monte, Argentina – Nelda L. Olivera – Journal of Arid Environments

Climatic conditions, soil fertility and atmospheric nitrogen deposition largely determine the structure and functioning of microbial communities in biocrust-dominated Mediterranean drylands – Raul Ochoa-Bon – Plant and Soil

The Bacterial and Fungal Diversity of an Aged PAH- and Heavy Metal-Contaminated Soil is Affected by Plant Cover and Edaphic Parameters – Amélia Bourceret – Microbial Ecology

Water and extremophile microbiome

Cable bacteria generate a firewall against euxinia in seasonally hypoxic basins – Dorina Seitaj – PNAS
Novel viral genomes identified from six metagenomes reveal wide distribution of archaeal viruses and high viral diversity in terrestrial hot springs – Sóley Ruth Gudbergsdóttir – Environmental Microbiology

Waste treatment microbiology

Characterization of microbial communities in water and biofilms along a large scale SWRO desalination facility: Site-specific prerequisite for biofouling treatments – Adi Levi – Desalination

Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans – Massimo C Pernice – The ISME Journal

Metabolomics

A Global Metabolomic Analysis of a Mammalian Host Infected with Bacillus anthracis
Chinh T.Q. Nguyen – Infection and Immunity

Sequencing techniques

Bioinformatic Suggestions on MiSeq-Based Microbial Community Analysis
Tatsuya Unno – Journal of Microbiology and Biotechnology

Bioinformatics and metagenomics

Differential analysis of biological networks – Da Ruan – BMC Bioinformatics

SPINGO: a rapid species-classifier for microbial amplicon sequences – Guy Allard – BMC Bioinformatics

DectICO: an alignment-free supervised metagenomic classification method based on feature extraction and dynamic selection – Xiao Ding – BMC Bioinformatics

Experimental Design and Bioinformatics Analysis for the Application of Metagenomics in Environmental Sciences and Biotechnology – Feng Ju and Tong Zhang – Environmental Science & Technology

A Comparison of Base-calling Algorithms for Illumina Sequencing Technology – Ashley Cacho – Briefings in Bioinformatics

Metabolomics

A Validated High Resolution Mass Spectrometry-based Approach for Metabolomic Fingerprinting of the Human Gut Phenotype – Julie Vanden Bussche – Analytical Chemistry

Microbes in the news

Should We Bank Our Own Stool? – Moises Velasquez-Manoff – New York Times

Researchers use gut bacteria composition to genetically classify colorectal tumors – EurekAlert

Bacteria take on stinky problem in Kenner – Christie Walton – Fox8Live

MSU faculty member earns grant award for biofilm methodology research: Darla Goeres was recently awarded a Burroughs Wellcome Innovation in Regulatory Science Award. – Montana State University

Biotech of the week: Enterome, the Leading French Microbiome Start-up – LaBiotech

Conference Coverage: ID week: Drug Resistance: What Happens Inside the Nose? – HCP Live

Antibiotic use and cancer risk: Repeat exposure poses harm: interview with Ben Boursi – Healio

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October 6, 2015

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Human gut microbiome

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

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

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

Models of microbiome research

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

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

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

Animal microbiome

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

Plant, root, and soil microbiome

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

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

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

Water microbiome

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

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

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

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

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

Extremophile microbiome

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

Metabolic networks, proteomics

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

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

Bioinformatics and metagenomics

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

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

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

Techniques

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

More microbiology

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

Microbes in the news

Georgia State Researcher Gets $1.35 Million to Study Effects of Common Food Additive on Body – Georgia State University
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October 2, 2015

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Human gut microbiome

Mucosa-Associated Faecalibacterium prausnitzii Phylotype Richness Is Reduced in Patients with Inflammatory Bowel Disease – Mireia Lopez-Siles – Applied and Environmental Microbiology

Comparison of Fecal Microbiota in Children with Autism Spectrum Disorders and Neurotypical Siblings in the Simons Simplex Collection – Joshua S. Son – PLOS ONE

Specific members of the predominant gut microbiota predict pouchitis following colectomy and IPAA in UC – Kathleen Machiels – Gut

Review: The Intestinal Microbiome in Bariatric Surgery Patients – Christine M. Peat – European Eating Disorders Review

Human urinary tract microbiome

Incontinence medication response relates to the female urinary microbiota – Krystal J. Thomas-White – International Urogynecology Journal

Animal models

In rats: N-3 Polyunsaturated Fatty Acids (PUFAs) Reverse the Impact of Early-Life Stress on the Gut Microbiota – Matteo M. Pusceddu – PLOS ONE

Table grape consumption reduces adiposity and markers of hepatic lipogenesis and alters gut microbiota in butter fat-fed mice – Jessie Baldwin – The Journal of Nutritional Biochemistry

In mice: Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut – Jinbao Yin – Ecotoxicology

Review: Changes to the Intestinal Microbiome With Parenteral Nutrition – Review of a Murine Model and Potential Clinical Implications – Farokh R. Demehri – Nutrition in Clinical Practice

Plant, root, and soil microbiology

Profile Changes in the Soil Microbial Community When Desert Becomes Oasis – Chen-hua Li – PLOS ONE

Water microbiology

The Ocean as a Global Reservoir of Antibiotic Resistance Genes – Stephen M. Hatosy – Applied and Environmental Microbiology

Diversity of Miscellaneous Crenarchaeotic Group archaea in freshwater karstic lakes and their segregation between planktonic and sediment habitats – Mireia Fillol – FEMS Microbiology Ecology

DGGE: Bacterial Diversity in Bohai Bay Solar Saltworks, China – Jiaojiao Zhang – Current Microbiology

Techniques

Quantitative Microbial Ecology through Stable Isotope Probing – Bruce A. Hungate – Applied and Environmental Microbiology

Bioinformatics

Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples – Nezar Noor Al-Hebshi – Journal of Oral Microbiology

Science, publishing, and career

Predatory publishers earned $75 million last year, study finds – John Bohannon – Science

‘Predatory’ open access: a longitudinal study of article volumes and market characteristics – Cenyu Shen and Bo-Christer Björk – BMC Medicine

Ten Simple Rules for Protecting Research Integrity – David M. Shaw, Thomas C. Erren – PLOS Computational Biology

Microbes in the news

How gut health affects cycling performance – Cycling Weekly

Microbial sampling starts in Cherokee Homes – Jordan Peccia – MicroBEnet

Why It Was Easier to Be Skinny in the 1980s – Olga Khazan – The Atlantic

How do we protect ourselves from Martian bacteria? – Anjana Ahuja – World Economic Forum
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