February 1, 2015

Ah, the revenge of being away from work: my in-box was bursting out of the seams with new papers. Today I am quickly catching up after being offline for just 3 days, and I will skip most formatting to save some time (e.g. I will only do the bare essentials, and won’t add the hyperlinks). Enjoy.

General microbiome

Review? Discovering Emergent Behavior of Host-Microbiome Interactions with Biomimetic Robotics – Keith C. Heyde, Warren C. Ruder – Biophysical Journal

Book: Microbiome Community Ecology – Muhammad Saleem – Springer Briefs in Ecology

Human oral microbiome

16S rRNA based microarray analysis of ten periodontal bacteria in patients with different forms of periodontitis – Nursen Topcuoglu, Guven Kulekci – Anaerobe

Human respiratory microbiome

Dynamics of the nasal microbiota in infancy: A prospective cohort study – Moana Mika – Journal of Allergy and Clinical Immunology

Review: The microbiome of the upper airways: focus on chronic rhinosinusitis – Thanit Chalermwatanachai – World Allergy Organization Journal

Human skin microbiome

Mapping axillary microbiota responsible for body odours using a culture-independent approach – Myriam Troccaz – Microbiome Journal

The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites – Ana M Misic – Microbiome Journal

Insights into bacterial colonization of intensive care patients’ skin: the effect of chlorhexidine daily bathing – N. Cassir – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

(see also Metagenomics) Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species – Sharon Greenblum – Cell

Gut microbiota composition correlates with changes in body fat content due to weight loss – M. Remely – Beneficial Microbes

Genetic Modifier of the Gut Microbiome, GvHD and Bacterial Translocation Following HSCT – Ahmad Rayes – Biology of Blood and Marrow Transplantation

A Pilot Study of Donor Enteral Human Milk to Modulate the Gut Microbiome in Children Receiving Stem Cell Transplant – Stella M. Davies – Biology of Blood and Marrow Transplantation

This might be review (no access from my location): Microbiome, peptide autoantibodies, and eating disorders: a missing link between gut and brain – Akio Inui – Nutrition

Oral Supplementation with L-Glutamine Alters Gut Microbiota of Obese and Overweight Human Adults: A Pilot Study – Alessandra Zanin Zambom de Souza – Nutrition

Review: Growth Promotion and Gut Microbiota: Insights from Antibiotic Use – Harald Brüssow – Environmental Microbiology

Hypothesis: An Agent-Based Modeling Framework for Evaluating Hypotheses on Risks for Developing Autism: Effects of the Gut Microbial Environment – Bronson Weston – Medical Hypotheses

Hypothesis: Gut feelings: A role for the intestinal microbiota in anorexia nervosa? – Susan C. Kleiman – International Journal of Eating Disorders

Review??? Beyond Model Systems: Super-Resolving the Subcellular Dynamics of Starch Digestion in the Human Gut Microbiome – Krishanthi S. Karunatilaka – Biophysical Journal

Review: Intestinal Microbiota And Diet in IBS: Causes, Consequences, or Epiphenomena? – Mirjana Rajilić-Stojanović – American Journal of Gastroenterology

Review: H. pylori and its modulation of gastrointestinal microbiota – Christian Schulz – Journal of Digestive Diseases

Review: Implication of Gut Microbiota in Nonalcoholic Fatty Liver Disease
Jerome Boursier – PLOS Pathogens

Review: The human gut microbiota with reference to autism spectrum disorder: considering the whole as more than a sum of its parts – Michael C. Toh and Emma Allen-Vercoe – Microbial Ecology in Health and Disease

Review: The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity – Ningwen Tai – Reviews in Endocrine and Metabolic Disorders

Review: Diet, Gut Microbiome, and Bone Health – Connie M. Weaver – Current Osteoporosis Reports

Review: Immunogenic properties of a probiotic component of the human gastrointestinal tract microbiota – I. A. Fedorova, V. N. Danilenko – Biology Bulletin Reviews

Animal models of microbiome

Intestinal Microbial Dysbiosis and Colonic Epithelial Cell Hyperproliferation by Dietary α-Mangostin is Independent of Mouse Strain – Fabiola Gutierrez-Orozco – Nutrients

Polyphenol-rich sorghum brans alter colon microbiota and impact species diversity and species richness after multiple bouts of dextran sodium sulfate-induced colitis
Lauren E. Ritchie – FEMS Microbiology Ecology

Effects of chronic exposure to environmentally relevant concentrations of waterborne depleted uranium on the digestive tract of zebrafish, Danio rerio – Starrlight Augustine – Journal of Environmental Radioactivity

Cross-Differentiation from the CD8 Lineage to CD4 T Cells in the Gut-Associated Microenvironment with a Nonessential Role of Microbiota – Jen Bon Lui – Cell Reports

Administration of probiotics Lactobacillus rhamnosus GG and Lactobacillus gasseri K7 during pregnancy and lactation changes mouse mesenteric lymph nodes and mammary gland microbiota – P. Treven- Journal of Dairy Science

Animal microbiome

First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing – Shuai Peng – Journal of Applied Genetics

Prepartum and Postpartum Rumen Fluid Microbiomes: Characterization and Correlation with Production Traits in Dairy Cows – Fabio S. Lima – Applied Environmental Microbiology

Relationship between honeybee nutrition and their microbial communities – Miriane Acosta Saraiva – Antonie van Leeuwenhoek

Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation – Gang Yang – Biochemical and Biophysical Research Communications

Microbiome affects egg carotenoid investment, nestling development and adult oxidative costs of reproduction in Great tits – Staffan Jacob – Functional Ecology

Review: Dietary fibre and the importance of the gut microbiota in feline nutrition: a review
Kristel Rochus – Nutrition Research Reviews

Plant microbiome

T Bacterial Communities Associated with Surfaces of Leafy Greens: Shift in Composition and Decrease in Richness over Time – Merete Wiken Dees – Applied Environmental Microbiology

Soil, rock, and sediment microbiome

Long-term forest soil warming alters microbial communities in temperate forest soils – Kristen M. DeAngelis – Frontiers in Microbiology

This one was submitted in June 2013, but just published: Soil microbial community structure and activity in a 100-year-old fertilization and crop rotation experiment – Cancan Zhao – Journal of Plant Ecology

Interrogation of Chesapeake Bay sediment microbial communities for intrinsic alkane-utilizing potential under anaerobic conditions – Jamie M. Johnson – FEMS Microbiology Ecology

Short-term effects of soil amendment with meadowfoam seed meal on soil microbial composition and function – Suphannika Intanon – Applied Soil Ecology

Molecular diversity of arbuscular mycorrhizal fungi at a large-scale antimony mining area in southern China – Yuan Wei – Journal of Environmental Sciences

Assessing Fungal Community Structure from Mineral Surfaces in Kartchner Caverns Using Multiplexed 454 Pyrosequencing – Michael Joe Vaughan – Microbial Ecology

Effects of increasing precipitation on soil microbial community composition and soil respiration in a temperate desert, Northwestern China – Gang Huang – Soil Biology and Biochemistry

Review: Microbial ecology of hot desert edaphic systems – Thulani P. Makhalanyane – FEMS Microbiology Reviews

Water microbiome

Synchronous shifts in dissolved organic carbon bioavailability and bacterial community responses over the course of an upwelling-driven phytoplankton bloom – Emma K. Wear – Limnology and Oceanography

Comparison of the microbial communities of hot springs waters and the microbial biofilms in the acidic geothermal area of Copahue (Neuquén, Argentina) – María Sofía Urbieta – Extremophiles

Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA) – Cassandre Sara Lazar – Environmental Microbiology

Methane oxidation pathways and associated methanotrophic communities in the water column of a tropical lake – Prosper K. Zigah – – Limnology and Oceanography

Seasonal assemblages and short-lived blooms in coastal north-west Atlantic Ocean bacterioplankton – Heba El-Swais – Environmental Microbiology

Environmental rather than spatial factors structure bacterioplankton communities in shallow lakes along a > 6000 km latitudinal gradient in South America – Caroline Souffreau – Environmental Microbiology

Microbial Contamination of Drinking Water and Human Health from Community Water Systems
Nicholas J. Ashbolt – Current Environmental Health Reports

Book Chapter: Microbial Bioprospecting in Marine Environments – Mariana Lozada, Hebe M. Dionisi – Hb25_Springer Handbook of Marine Biotechnology

Bioreactor microbiome

Long-term monitoring reveals stable and remarkably similar microbial communities in parallel full-scale biogas reactors digesting energy crops – Rico Lucas – FEMS Microbiology Ecology

The fate of oxytetracycline in two-phase and single-phase anaerobic cattle manure digesters and its effects on microbial communities – Çağrı Akyol – Journal of Chemical Technology and Biotechnology

Identification of the microbial community composition and structure of coal-mine wastewater treatment plants – Qiao Ma – Microbiological Research

New steady-state microbial community compositions and process performances in
biogas reactors induced by temperature disturbances – Gang Luo – Biotechnology for Biofuels


Diversity of Methane-Cycling Archaea in Hydrothermal Sediment Investigated by General and Group-Specific PCR Primers – Mark A. Lever and Andreas P. Teske – Applied Environmental Microbiology

Ecophysiology of uncultivated marine euryarchaea is linked to particulate organic matter – WIlliam D Orsi – ISME Journal


Integrating Multi-omic features exploiting Chromosome Conformation Capture data – Ivan Merelli – Frontiers in Genetics

Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach – Philippe Rocca-Serra – Database

Koonkie: An Automated Software Tool for Processing Environmental
Sequence Information using Hadoop – Dongjae Kim – ASE360

MetAmp: combining amplicon data from multiple markers for OTU analysis – Ilya Y. Zhbannikov,, James A. Foster – Bioinformatics

MetaAB – A Novel Abundance-Based Binning Approach for Metagenomic Sequences
Van-Vinh Le – Nature of Computation and Communication
Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering

NCBI BLAST+ integrated into Galaxy – Peter J. A. Cock – BioRxiv


Extensive Strain-Level Copy-Number Variation across Human Gut Microbiome Species – Sharon Greenblum – Cell

Integrated metagenomics and network analysis of soil microbial community of the forest timberline – Junjun Ding – Scientific Reports

Book Chapter: Marine Sponge Metagenomics – Valliappan Karuppiah, Zhiyong Li – Hb25_Springer Handbook of Marine Biotechnology

Ecological and genetic interactions between cyanobacteria and viruses in a low-O2 mat community inferred through metagenomics and metatranscriptomics – Alexander A. Voorhies – Environmental Microbiology

Metagenomic analysis reveals adaptations to a cold adapted lifestyle in a low temperature acid mine drainage stream – Maria Liljeqvist – FEMS Microbiology Ecology

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes – Manuel Kleiner – BMC Genomics

First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking – Yuji Sekiguchi – PeerJ

The effects of variable sample biomass on comparative metagenomics – Meghan Chafee – Environmental Microbiology

Review: Functional genomic and metagenomic approaches to understanding gut microbiota–animal mutualism – Sang Sun Yoon – Current Opinion in Microbiology

Book Chapter: Marine Metagenome and Supporting Technology – Tetsushi Mori – Hb25_Springer Handbook of Marine Biotechnology

Transcriptomics, metabolomics

Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen – Xin Dai – Applied Environmental Microbiology

Genomic Potential for Polysaccharide Deconstruction in Bacteria – Renaud Berlemont and Adam C. Martiny – Applied Environmental Microbiology

Microbial dark matter ecogenomics reveals complex synergistic networks in a methanogenic bioreactor – Masaru K Nobu – ISME Journal

Perturbations of tyrosine metabolism promote the indolepyruvate pathway via tryptophan in host and microbiome – Ilya Gertsman – Molecular Genetics and Metabolism

Gut Symbionts from Distinct Hosts Exhibit Genotoxic Activity via Divergent Colibactin Biosynthesis Pathways – Philipp Engel – Applied Environmental Microbiology

Transcriptome analyses to investigate symbiotic relationships between marine – Sergio Balzano – Frontiers in Microbiology

Perturbations of tyrosine metabolism promote the indolepyruvate pathway via tryptophan in host and microbiome – Ilya Gertsman – Molecular Genetics and Metabolism

Human metabolic, mineral, and microbiota fluctuations across daily nutritional intake visualized by a data-driven approach – Takuma Misawa – Journal of Proteome Research

Review: Prospects and challenges for fungal metatranscriptomics of complex communities – Cheryl R. Kuske – Fungal Ecology

Microbial Ecology

Disturbance opens recruitment sites for bacterial colonization – David Vuono – BioRxiv

Review: High-throughput DNA barcoding for ecological network studies – Hirokazu Toju – Population Ecology

Book Chapter: For Three Billion Years, Microorganisms Were the Only Inhabitants of the Earth
Jean-Claude Bertrand – Environmental Microbiology: Fundamentals and Applications

Book Chapter: Microbiome Ecosystem Ecology: Unseen Majority in an Anthropogenic Ecosystem- Muhammad Saleem – Microbiome Community Ecology

More microbes

Introduction to a special issue of PLOS Pathogens: The Importance of Pathogen Load – Aubrey J. Cunnington – PLOS Pathogens

Microbes in the news

Satire: Secret Microbiome Forensic Study Reveals DeflateGate Culprit – Megabiome.net

Secret microbiome forensic study reveals #deflategate culprit

Among gut microbes, strains, not just species, matter – MedicalXpress

Analysis Highlights Strain Diversity in Gut Microbiome – GenomeWeb

Jonathan Eisen and Jessica Richman on the Microbiome – Kevin Bonham – Scientific American

Part-Time Pooping: A New Way to Make an Extra $13,000 a Year – Everyday Health

OpenBiome will pay for poo – Helen Clark – GizMag

January 2015 Update on American Gut, British Gut and Australian Gut Human Microbiome Projects – IBS Impact

The Microbiome – New Research On Inflammatory Bowel Disease May Foreshadow Autism? – Teresa Conrick – Age of Autism

The microbiome of the upper airways: focus on chronic rhinosinusitis – 7th Space

Germ Theory: What You May Not Know About The Bacteria Crawling Around Your Bathroom – Justin Caba – Medical Daily

Altered gut microbiota seen in patients with psoriatic arthritis – Healio.com

The Human Microbiome: Biomedical Implications and Birth of a Market – Overview – PRNewsWIre

Meet Dr. Armpit, changing body odor with bacteria – Fast Company

Gut bacteria byproduct linked to chronic kidney disease for the first time – Medical Xpress

Does draft beer give you a worse hangover? We came across people from the beer industry and beer drinkers who claimed the bacteria in those lines contributes to a hangover. – Jace Larson – Click 2 Houston

Bik’s Picks

Face blindness predicted by structural differences in the brain, Stanford neuroscientists discover – Leslie Willoughby – Stanford News



One thought on “February 1, 2015

  1. Hurrah! In the end I got a blog from where I know how to truly
    get valuable information regarding my study and knowledge.


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