Category Archives: Human oral

January 19, 2016

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Microbiota manipulation during stem cell transplants, meh-crobial diversity in digestive tract of two sheep breeds, eukaryotes within pitcher plants,  South Atlantic Ocean, and soil affected by the 2011 Japan Tsunami.

Events

ISME16, Montreal, Canada, 21 – 26 August 2016. Registration and Submissions now open. The deadline for submitting your abstract is 18 March.

ASM Career Development Grants for Postdoctoral Women – up to 4 awards of $1,500 each. Deadline for Nominations: February 1, 2016.

Fellowships by L’Oréal USA For Women In Science. Deadline Feb 5, 2016. Program awards five women postdoctoral scientists annually with grants of $60,000 each, in any specialty.

Human oral microbiome

Salivary bacterial fingerprints of established oral disease revealed by the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technique – Daniel Belstrøm – Journal of Oral Microbiology

Human gut microbiome

Sleep quality and the treatment of intestinal microbiota imbalance in Chronic Fatigue Syndrome: A pilot study – Melinda L. Jackson – Sleep Science

Fecal microbiota transplantation: A ‘How-To’ guide for nurses – Sharyn Leis – Collegian Journal

Review: Microbiota Manipulation With Prebiotics and Probiotics in Patients Undergoing Stem Cell Transplantation – Tessa M. Andermann – Current Hematologic Malignancy Reports

Review: Epigenetic Regulation of Enteric Neurotransmission by Gut Bacteria – Tor C. Savidge – Frontiers in Cellular Neuroscience

Bioreactor and animal models

Microbial Metabolism Shifts Towards an Adverse Profile with Supplementary Iron in the TIM-2 In vitro Model of the Human Colon – Guus A. M. Kortman – Frontiers in Microbiology

Video: A Novel Bioreactor for High Density Cultivation of Diverse Microbial Communities – Jacob R. Price – JOVE

Atlantic Salmon (Salmo salar L.) Gastrointestinal Microbial Community Dynamics in Relation to Digesta Properties and Diet – Kamarul Zaman Zarkasi – Microbial Ecology

Animal microbiome

Microbial diversity in the digestive tract of two different breeds of sheep – J.-L. Douglas – Journal of Applied Microbiology

Dynamics of Bacterial Community Composition in the Malaria Mosquito’s Epithelia – Majoline T. Tchioffo – Frontiers in Microbiology

Microbiota Plays a Role in Oral Immune Priming in Tribolium castaneum – Momir Futo – Frontiers in Microbiology

Plant, root, and soil microbiome

Dynamics of Viral Abundance and Diversity in a Sphagnum-Dominated Peatland: Temporal Fluctuations Prevail Over Habitat – Flore Ballaud – Frontiers in Microbiology

Biogeographic barriers drive co-diversification within associated eukaryotes of the Sarracenia alata pitcher plant system – Jordan D. Satler – PeerJ

Expanding our Understanding of the Seaweed Holobiont: RNA Viruses of the Red Alga Delisea pulchra – Tim Lachnit – Frontiers in Microbiology

New Methods To Unravel Rhizosphere Processes – Eva Oburger – Trends in Plant Science

Soil microbial responses to forest floor litter manipulation and nitrogen addition in a mixed-wood forest of northern China – Xiao-Lu Sun – Scientific Reports

Unraveling the Functions of the Macroalgal Microbiome – Ravindra Pal Singh – Frontiers in Microbiology

Water and extremophile microbiome

Diversity and bioprospection of fungal community present in oligotrophic soil of continental Antarctica – Valéria M. Godinho – Extremophiles

Novel Barite Chimneys at the Loki’s Castle Vent Field Shed Light on Key Factors Shaping Microbial Communities and Functions in Hydrothermal Systems – Ida H. Steen – Frontiers in Microbiology

High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes – Marion H. Stagars – Frontiers in Microbiology

Nutrient limitation of microbial phototrophs on a debris-covered glacier – J.L. Darcy – Soil Biology and Biochemistry

Large-scale distribution of microbial and viral populations in the South Atlantic Ocean – Daniele De Corte – Environmental Microbiology Reports

Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities – Anna Hanke – Frontiers in Microbiology

A Lipid-Accumulating Alga Maintains Growth in Outdoor, Alkaliphilic Raceway Pond with Mixed Microbial Communities – Tisza A. S. Bell – Frontiers in Microbiology

Genomic Reconstruction of an Uncultured Hydrothermal Vent Gammaproteobacterial Methanotroph (Family Methylothermaceae) Indicates Multiple Adaptations to Oxygen Limitation – Connor T. Skennerton – Frontiers in Microbiology

Genomic and metagenomic analysis of microbes in a soil environment affected by the 2011 Great East Japan Earthquake tsunami – Satoshi Hiraoka – BMC Genomics

Oil reservoir microbiome

Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs – Ping Hu – mBio

Food microbiology

Dynamic changes in microbiota and mycobiota during spontaneous ‘Vino Santo Trentino’ fermentation – Irene Stefanini – Microbial Biotechnology

Other microbiology and techniques

Perspective: Adapting Koch’s postulates – Allyson L. Byrd, Julia Segre – Science

Depletion of human DNA in spiked clinical specimens to improve the sensitivity of pathogen detection by next generation sequencing – Mohammad R. Hasan – Journal of Clinical Microbiology

Evaluation of a new device to simplify and standardize stool sample preparation for viral molecular testing with limited hands-on-time – Linda Feghoul – Journal of Clinical Microbiology

Review: Polymicrobial Biofilm Studies: from Basic Science to Biofilm Control – Hubertine ME Willems – Current Oral Health Reports

Review: Laser microdissection: A promising tool for exploring microorganisms and their interactions with hosts – Oleg V. Podgorny – Journal of Microbiological Methods

Book: Applications of Mass Spectrometry in Microbiology – Plamen Demirev, Todd R Sandrin – Springer

Metagenomics and bioinformatics

Searching more genomic sequence with less memory for fast and accurate metagenomic profiling – Shea N Gardner – bioRxiv

An evaluation of the accuracy and speed of metagenome analysis tools – Stinus Lindgreen – Scientific Reports

Motif-based text mining of microbial metagenome redundancy profiling data for disease classification – Yin Wang – BioMed Research International

Metabolic pathways

Metabolic traits of an uncultured archaeal lineage -MSBL1- from brine pools of the Red Sea – Romano Mwirichia – Scientific Reports

Microbes in the news

Looking at the Microbiota to Improve Intestinal Transplantation Results – Jeannette Y. Wick – HCP Live

Why do I have to share my body with so many bugs? – Michael Mosley – BBC

How Bitter Taste Receptors Defend the Body against Bacteria – Robert J Lee – Scientific American

White Paper: The Future of Microbiome Research: Out of the Lab and Into the Clinic – Global Engage

How chicory may help fight plague bacteria – Jason Tetro – Popular Science

Lethal bacteria in Christmas Island feral cats sparks warning (Leptospira) – Nicolas Perpitch – ABC Australia

Microbes and art

Subvisual Subway: The Art of New York City’s Bacterial World – Emily Driscoll – Science Friday

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January 16, 2016

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Gut microbiota in acute malnutrition, social behavior and the chimpanzee pan-microbiome, arctic marine fungi, and learning ecological networks.

General microbiome

Immune-Microbiota Interactions: Dysbiosis as a Global Health Issue – Alan C. Logan – Current Allergy and Asthma Reports

Human oral microbiome

Long-term prospective cohort study on dental implants: clinical and microbiological parameters – Henri Tenenbaum – Clinical Oral Implants Research

Human reproductive tract microbiome

Alterations in the Genital Microbiota in Women With Spinal Cord Injury – Pires, Cristhiane V.G. – Obstetrics & Gynecology

Human gut microbiome

Gut Microbiota in Children Hospitalized with Oedematous and Non-Oedematous Severe Acute Malnutrition in Uganda – Kia Hee Schultz Kristensen – PLOS Neglected Tropical Diseases

Editorial: Confounding Effects of Metformin on the Human Gut Microbiome in Type 2 Diabetes – Adil Mardinoglu – Cell Metabolism

Review: Impact of high fat diets, prebiotics and probiotics on gut microbiota and immune function, with relevance to elderly populations – Yue Liu – Nutrition and Aging

Review: Transkingdom control of viral infection and immunity in the mammalian intestine – Julie K. Pfeiffer – Science

Review: Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality – Rosemarie De Weirdt – NPJ Biofilms and Microbiomes

Animal models

In rats: Alternating or continuous exposure to cafeteria diet leads to similar shifts in gut microbiota compared to chow diet – Nadeem O. Kaakoush – Molecular Nutrition & Food Research

In mice: Streptomycin treatment alters the intestinal microbiome, pulmonary T cell profile and airway hyperresponsiveness in a cystic fibrosis mouse model – Mark Bazett – Scientific Reports

Animal microbiome

Social behavior shapes the chimpanzee pan-microbiome – Andrew H. Moeller – Science Advances

Environmental drivers of microbial community shifts in the giant barrel sponge, Xestospongia muta, over a shallow to mesophotic depth gradient – Kathleen M. Morrow – Environmental Microbiology

Feeding cessation alters host morphology and bacterial communities in the ascidian Pseudodistoma crucigaster – Susanna López-Legentil – Frontiers in Zoology

Plant, root, and soil microbiome

Uncultivated margins are source of soil microbial diversity in an agricultural landscape –
Luciana D’Acunto – Agriculture, Ecosystems & Environment

Editorial: Deep influence of soil microbes – Karl Gruber – Nature Plants

Review: Soil microbes and community coalescence – Matthias C. Rillig – Pedobiologia

Water and extremophile microbiome

Linkages between mineralogy, fluid chemistry, and microbial communities within hydrothermal chimneys from the Endeavor Segment, Juan de Fuca Ridge – T. J. Lin – Geochemistry, Geophysiscs, Geosystems

Exploration of microbial diversity and community structure of Lonar Lake: the only hypersaline meteorite crater lake within basalt rock – Dhiraj Paul – Frontiers in Microbiology

Vertical segregation and phylogenetic characterization of ammonia-oxidizing bacteria and archaea in the sediment of a freshwater aquaculture pond – Shimin Lu – Frontiers in Microbiology

Chytrids Dominate Arctic Marine Fungal Communities – B.T. Hassett – Environmental Microbiology

Built environment microbiome

Bacterial Monitoring in the International Space Station-“Kibo” Based on rRNA Gene Sequence – Nobuyasu Yamaguchi – Transactions of the Japan Society for Aeronautical and Space Sciences

Metagenomics and bioinformatics

Safe and complete contig assembly via omnitigs – Alexandru I. Tomescu – ArXiv

More microbiology and ecology

How clonal are bacteria over time? – B. Jesse Shapiro – BioRxiv

Transcription Factors Exhibit Differential Conservation in Bacteria with Reduced Genomes – Edgardo Galán-Vásquez – PLOS ONE

Learning Ecological Networks from Next-Generation Sequencing Data – Corinne Vacher – Advances in Ecological Research

Microbes in the news

Chimps Share Microbes When Socializing – Kate Yandell – The Scientist

How Your Social Life Changes Your Microbiome – Ed Yong – The Atlantic

Social Contact Helps Beneficial Gut Bacteria Spread – Brian Handwerk – Smithsonian

Prevent severe diarrhea by controlling levels of specific gut bacteria – Bel Marra Health

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January 14, 2016

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Sorry for a late post today – I had a lot of meetings. Here is what I found:

Gut microbiota shaped via fecal microRNA, the microgenderome, dysbiosis in Vitiligo skin lesions, metatranscriptomics, and an 18th century Yersinia pestis.

General microbiome

Perspective: Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease – Niv Zmora – Cell Host & Microbe

The Human Microbiome: Opportunities for Dynamics, Systems, and Control
(based on the IFAC blog post Translate or Die) – Travis E. Gibson – Submitted to ACC 2016

Human skin microbiome

Microbial community profiling shows dysbiosis in the lesional skin of Vitiligo subjects – Parul Ganju – Scientific Reports

Human oral microbiome

Diversity and homogeneity of oral microbiota in healthy Korean pre-school children using pyrosequencing – Soo Eon Lee – Acta Odontologica Scandinavica

Short-term effects of povidone iodine and sodium fluoride therapy on plaque levels and microbiome diversity – C Reilly – Oral Diseases

Commentary: A new association for the oral metagenome – Nicholas S Jakubovics – Oral Diseases

Human vaginal microbiome

Review: Vaginal microbiota and microbiome:- Role in health and disease – Dr Amit A. Rangari – Indian Journal of Basic and Applied Medical Research;

Human gut microbiome

Support for the Microgenderome: Associations in a Human Clinical Population – Amy Wallis – Scientific Reports

Impact of increasing fruit and vegetables and flavonoid intake on the human gut microbiota – Annett Klinder – Food & Function

Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficile – Ranjit Kumar – BMC Microbiology

Review: The microbiome and its implications in intestinal transplantation – Kroemer, Alexander – Current Opinion in Organ Transplantation

Animal models

Genetic and Metabolic Signals during Acute Enteric Bacterial Infection Alter the Microbiota and Drive Progression to Chronic Inflammatory Disease – Karishma Kamdar – Cell Host & Microbe

The Host Shapes the Gut Microbiota via Fecal MicroRNA – Shirong Liu – Cell Host & Microbe

Animal microbiome

The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica – Ngare Wilkinson – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Culturable endophytic bacterial communities associated with field grown soybean – Karla Bianca de Almeida Lopes – Journal of Applied Microbiology

Historical precipitation predictably alters the shape and magnitude of microbial functional response to soil moisture – Colin Averill – Global Change Biology

Water and waste microbiome

Development of new host-specific Bacteroides qPCRs for the identification of fecal contamination sources in water – Marta Gómez-Doñate – Microbiology Open

Bacterial diversity in oil-polluted marine coastal sediments – Alejandro Acosta-González – Current Opinion in Biotechnology

Spatial and temporal variability of bacterial communities in high alpine water spring sediments – Alfonso Esposito – Research in Microbiology

Biogeochemical, Isotopic and Bacterial Distributions Trace Oceanic Abyssal Circulation – Angelo Rubino – PLOS ONE

Metagenomics, metatranscriptomics, and bioinformatics

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus – Kirsten I Bos – BioRxiv

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality – Yue Jiang – BMC Microbiome Journal

Viral metagenomics and blood safety – V. Sauvage – Transfusion Clinique et Biologique

Microbes in the news

Does our Microbiome Control Us or Do We Control It? – Dina Fine Maron – Scientific American

Your gut’s trick for controlling the bacteria that live in it – New Scientist

Mammals shape their microbiome to prevent disease – Science Codex

Low-Fiber Diets Cause Waves of Extinction in the Gut – Ed Yong – The Atlantic

Bad diets today can alter our great-great-grandkids’ biology – Katherine Ellen Foley – Quartz

Thoughtful and balanced comparison: mothur and QIIME – Pat Schloss – Mothur blog

Modifying the structure of wood alters plant microbiome – Science Daily

Gut Microbiome Similar in Formula- and Combination-Fed Babies – Troy Brown – MedScape

Eglin medical group first to find bacteria unseen in humans: Borrelia turicatae – Ilka Cole – US Air Force

Protecting the infant microbiome – Kathryn Kos – Examiner

Microbiology and art

Sunshine and microbiology inspire Reading artist’s work – Francesca Perryman – Get Reading

Science, publishing, and career

Re: Your Recent Email to Your Professor: Students who use emojis in their emails and write “heeeeelp!” in the subject line don’t necessarily know better.  – Paul T. Corrigan and Cameron Hunt McNabb – Inside Higher Education

ORCID: Publishers embrace scheme to end name confusion – John Bohannon – Science

Give teachers a physics test from a woman and they’ll give her worse grades – John Timmer – Ars Technica

Astronomy’s snowballing sexual harassment scandal picks up even more cases – Rachel Feltman – Washington Post

Bik’s Picks

Inside the Eye: Nature’s Most Exquisite Creation – Ed Yong – National Geographic
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January 12, 2016

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The ecology of microbiome research (in the new journal Nature Microbiology), gut microbiome of infants, dentition status and teeth microbes, human impact on corals, metagenomics, CRISPRs, rainforest and desert soils, and tropical oceans.

General microbiome

An assessment of US microbiome research – Elizabeth Stulberg – Nature Microbiology

Microbiome: Ecology of stable gut communities – Luke McNally – Nature Microbiology

Pregnancy and birth microbiome

Association of Cesarean Delivery and Formula Supplementation With the Intestinal Microbiome of 6-Week-Old Infants – Juliette C. Madan – JAMA Pediatrics

Human oral microbiome

Supragingival Microbial Profiles of Permanent and Deciduous Teeth in Children with Mixed Dentition – Weihua Shi – PLOS ONE

Human gut microbiome

Human Gut Bacteria Are Sensitive to Melatonin and Express Endogenous Circadian Rhythmicity – Jiffin K. Paulose – PLOS ONE

A New High-Throughput Approach to Genotype Ancient Human Gastrointestinal Parasites – Nathalie M. L. Côté – PLOS ONE

Intestinal Microbiota in Patients with Spinal Cord Injury – Bilgi Gungor – PLOS ONE

Editorial: A Potential Role for Host- Microbe Dysbiosis in Enteropathy Associated with HIV Infection – Michael D. George – Primary & Acquired Immunodeficiency Research

Review: The obese gut microbiome across the epidemiologic transition – Lara R. Dugas – Emerging Themes in Epidemiology

Animal microbiome

Obligate bacterial mutualists evolving from environmental bacteria in natural insect populations – Takahiro Hosokawa – Nature Microbiology

The Microbiome of Ehrlichia-Infected and Uninfected Lone Star Ticks (Amblyomma americanum) – R. T. Trout Fryxell – PLOS ONE

Coral microbial community dynamics in response to anthropogenic impacts near a major city in the central Red Sea – Maren Ziegler – Marine Pollution Bulletin

Application of Faecalibacterium 16S rDNA genetic marker for accurate identification of duck faeces – Da Sun – Environmental Science and Pollution Research

Review: Understanding the canine intestinal microbiota and its modification by pro-, pre- and synbiotics – what is the evidence? – Silke Schmitz – Veterinary Medicine and Science

Plant, root, and soil microbiome

Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest – Julia Elidia Lima-Perim – PLOS ONE

Corky root severity, root knot nematode galling and microbial communities in soil, rhizosphere and rhizoplane in organic and conventional greenhouse compartments –
Ariena H.C. van Bruggen – Applied Soil Ecology

Metacommunity analysis of amoeboid protists in grassland soils – Anna Maria Fiore-Donno – Scientific Reports

Microbial communities of buried soils of the Tsaritsyn Defense Line (1718–1720) – T. S. Demkina – Soil Biology

Perspective: Exploring rhizospheric interactions for agricultural sustainability: The need of integrative research on multi-trophic interactions – Rama Kant Dubey – Journal of Cleaner Production

Water microbiome

Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations – Irina N. Shilova – PLOS ONE

Low diversity of planktonic bacteria in the tropical ocean – Mathias Milici – Scientific Reports

Out of thin air: Microbial utilization of atmospheric gaseous organics in the surface ocean – Jesus M. Arrieta – Frontiers in Microbiology

Elevated nutrients change bacterial community composition and connectivity: high throughput sequencing of young marine biofilms – Jasmin C. Lawes – Biofouling

Waste microbiology

Dynamics of bacterial populations during bench-scale bioremediation of oily seawater and desert soil bioaugmented with coastal microbial mats – Nidaa Ali – Microbial Biotechnology

Sequential Changes of Microbial Community Composition During Biological Wastewater Treatment in Single Unit Waste Stabilization System – Subhasis Sarkar – Waste and Biomass Valorization

Diversity and interactions of microbial functional genes under differing environmental conditions: insights from a membrane bioreactor and an oxidation ditch – Yu Xia – Scientific Reports

Food microbiology

Investigation of chocolate produced from four different Brazilian varieties of cocoa (Theobroma cacao L.) inoculated with Saccharomyces cerevisiae – Aline Galvão Tavares Menezesa – Food Research International

Microbial diversity and metabolite composition of Belgian red-brown acidic ales – Isabel Snauwaert – International Journal of Food Microbiology

Metagenomics, CRISPRs, viruses, and bioinformatics

Computational prediction of CRISPR cassettes in gut metagenome samples from Chinese type-2 diabetic patients and healthy controls – Tatiana C. Mangericao – BMC Systems Biology

Identification of physical interactions between genomic regions by enChIP-Seq – Toshitsugu Fujita – BioRxiv

Metaviromics of Namib Desert Salt Pans: A Novel Lineage of Haloarchaeal Salterproviruses and a Rich Source of ssDNA Viruses – Evelien M. Adriaenssens – MDPI Viruses

A novel semi-supervised algorithm for the taxonomic assignment of metagenomic reads – Vinh Van Le – BMC Bioinformatics

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations – Matthew L Bendall – The ISME Journal

Techniques in microbiology

The 6th International Conference on Analysis of Microbial Cells at the Single Cell Level, Retz, Austria, 19-22 July, 2015 – Nina Bydlinski – New Biotechnology

Microbes in the news

Microbe Cells Don’t Outnumber Your Own – Marissa Fessenden – Smithsonian

Getting to know the vagina: Microbiomes and our health – Daniel Vosberg – McGillDaily

Acidification affects the ability of bacteria to clean our oceans – Phys.org

Science, publishing, and career

Do prestigious science journals attract bad science? – Julia Belluz – Vox

Female professors are woefully outnumbered at med schools nationwide – Melissa Bailey – STAT News
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January 8, 2016

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Breast milk microbiota profiles, what did the Romans ever do for us, it was only a matter of thyme, and going down the wrong clay.

Pregnancy and birth

Human milk microbiota profiles in relation to birthing method, gestation and infant gender – Camilla Urbaniak – Microbiome

Early Gut Colonization of Preterm Infants: Effect of Enteral Feeding Tubes – Gómez, Marta – Journal of Pediatric Gastroenterology and Nutrition

Review: Role of the Placenta in Preterm Birth: A Review – Terry K. Morgan – American Journal of Perinatology

Human oral microbiome

Long-term efficacy of microbiology-driven periodontal laser-assisted therapy – F. S. Martelli – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Human parasites in the Roman World: health consequences of conquering an empire – Piers D. Mitchell – Parasitology

Animal models

Microbiota-induced obesity requires farnesoid X receptor – Ava Parséus – Gut

The Gut Microbiome Is Altered in a Letrozole-Induced Mouse Model of Polycystic Ovary Syndrome – Scott T. Kelley – PLOS ONE

Animal microbiome

Heterogeneous size datasets of broiler intestinal microbial communities can be analyzed without normalization – I. Aranda-Olmedo – Poultry Science

Plant, root, and soil microbiome

Assessing Bacterial Diversity in the Rhizosphere of Thymus zygis Growing in the Sierra Nevada National Park (Spain) through Culture-Dependent and Independent Approaches
Javier Pascual – PLOS ONE

Image-based modelling of nutrient movement in and around the rhizosphere – Keith R. Daly – Journal of Experimental Botany

Unearthing the Antibacterial Mechanism of Medicinal Clay: A Geochemical Approach to Combating Antibiotic Resistance – Keith D. Morrison – Scientific Reports

Water and waste microbiology

Virome-associated antibiotic-resistance genes in an experimental aquaculture facility – Stefano Colombo – FEMS Microbiology Ecology

Biodiversity patterns of plankton assemblages at the extremes of the Red Sea – J.K. Pearman – FEMS Microbiology Ecology

Food microbiology

Taxonomic analysis of the microbial community in stored sugar beets using high-throughput sequencing of different marker genes – Sebastian Liebe – FEMS Microbiology Ecology

Bioinformatics and metagenomics

Antibiotic resistance genes across a wide variety of metagenomes – David Fitzpatrick – FEMS Microbiology Ecology

Microbes in the news

You’re Probably Not Mostly Microbes – Ed Yong – The Atlantic

Scientists discover how blue and green clays kill bacteria – National Science Foundation

Heartburn pills may help grow infection-causing bacteria in gut – Lisa Rapaport – News Daily

Good Bacteria In, Bad Bacteria Out: Biofilms In Water Pipes Filter Dangerous Pathogens Out Of Drinking Water – Lizette Borreli – Medical Daily

The Next Food Fad Is Coming: Feed Your Microbiome – Andrea Hayley, Epoch Times

Enterome Announces Collaboration with Johnson & Johnson Innovation Focused on the Discovery of Novel Targets and Therapeutics for Crohn’s Disease – PR Newswire

From the gut to the eye: commensal microbes as potential triggers of autoimmune uveitis – Atlas of Science

Changes coming with QIIME 2 – Greg Caporaso – Qiime

Science, publishing, and career

DATA CHECK: For female scientists, mixed funding results at U.S. agencies – Jeffrey Mervis – Science
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January 7, 2016

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A new estimate of the ratio microbial:human cells in our bodies, a 5300-year old Helicobacter genome, antibiotics alter bile metabolism, microbiota from 59 bird species, and fecal contamination of Kathmandu drinking water.

Events

3rd Microbiome R&D and Business Collaboration Forum: Europe, which will take place in London, on the 11th and 12th of April, 2016. Early registration closes Jan 15th.

Mysterious Microbes Webinar Series 1 of 3: Microbes and the miracle of compost tea, with Noah Fierer and Ryan Heiland, on Jan 14. Learn how and why microbes are the natural secret to green lawns, lush flowers, and abundant produce

General human microbiome

Revised estimates for the number of human and bacteria cells in the body – Ron Sender – bioRxiv

Review: The human microbiota: the role of microbial communities in health and disease – Luz Elena Botero – Acta Biologica Columbiana

Pregnancy and birth microbiome

A comparative study of bifidobacteria in human babies and adults – Shadi Khonsari – Bioscience of Microbiota, Food and Health

Human oral microbiome

Salivary Antimicrobial Peptides in Early Detection of Periodontitis – Güliz N. Güncü – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

The 5300-year-old Helicobacter pylori genome of the Iceman – Frank Maixner – Science

Microbiome animal and other models

Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine – Casey M. Theriot – mSphere

The Gut Microbiota Reduces Colonization of the Mesenteric Lymph Nodes and IL-12-Independent IFN-γ Production During Salmonella Infection – María Fernández-Santoscoy – Frontiers in Cellular and Infection Microbiology

Steering Endogenous Butyrate Production in the Intestinal Tract of Broilers as a Tool to Improve Gut Health – Lonneke Onrust – Frontiers in Veterinary Science

Animal microbiome

Comparative Gut Microbiota of 59 Neotropical Bird Species – Sarah M. Hird – Frontiers in Microbiology

Plant, root, and soil microbiome

Potential Activity, Size, and Structure of Sulfate-Reducing Microbial Communities in an Exposed, Grazed and a Sheltered, Non-Grazed Mangrove Stand at the Red Sea Coast –
Melike Balk – Frontiers in Microbiology

Bacterial endophytes from wild and ancient maize are able to suppress the fungal pathogen Sclerotinia homoeocarpa – Hanan R. Shehata – Journal of Applied Microbiology

High throughput multiplex real time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants – Gerald Otti – Journal of Applied Microbiology

Methods for Baiting and Enriching Fungus-Feeding (Mycophagous) Rhizosphere Bacteria  – Max-Bernhard Ballhausen – Frontiers in Microbiology

Cucumber Rhizosphere Microbial Community Response to Biocontrol Agent Bacillus subtilis B068150 – Lihua Li – MDPI Agriculture

Water and waste microbiome

Bacterial diversity in water samples from uranium wastes as demonstrated by 16S rDNA and ribosomal intergenic spacer amplification retrievals – Galina Radeva – Canadian Journal of Microbiology

Master thesis: Evaluation of Two Culture-Independent Methods for Quantification of the Fraction of K-and r-Strategists within Water Microbial Communities – Brandsegg, Hege – Norges teknisk-naturvitenskapelige universitet

Built environment microbiome

The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water – Abhilasha Karkey – PLOS Neglected Tropical Diseases

Application of the Environmental Relative Moldiness Index in Finland – Martin Täubel – Applied and Environmental Microbiology

Food microbiology

Review: Phage-Host Interactions of Cheese-Making Lactic Acid Bacteria – Jennifer Mahony – Annual Review of Food Science and Technology

Metagenomics and bioinformatics

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics – Alejandra Escobar-Zepeda – Frontiers in Genetics

Science, publishing, and career

Peer review: tips from field experts for junior reviewers – Sabina Alam – BMC Medicine

Microbes in the news

Gut bacteria from Otzi the Iceman reveals our intimate ties to one microbe – Rachel Feltman – Washington Post

Scientists unearth bacteria from stomach of 5,300-year-old iceman – Carl Zimmer – StatNews

The Famous Ancient “Iceman” Had Ulcer Bacteria In His Gut – Dan Vergano – BuzzFeed

High Stress Environments May Lead To Unhealthy Gut Microbiomes: How To Protect Yourself From The Consequences – Lecia Bushak – Medical Daily

Antibiotics Pave Way for C. Diff Infections – North Carolina State University

Jackson Laboratory Hosted Microbiome Symposium Related to Cancer and Immunology – Lexology

The Bacteria That May Be Causing Your Nasty Cold. “The most common one of them in Mycoplasma Pneumoniae Infection,” Martin explained. – Fox29

Bik’s Picks

A “Pedi” Cures All: Toenail Trimming and the Treatment of Ulcerative Dermatitis in Mice – Sean C. Adams – PLOS ONE
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December 31, 2015

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Last post of the year! Wishing you and all microbiomes a great, successful and healthy 2016!

Dead or alive in the sinus microbiome, early life exercise, feather degrading bacteria in the house sparrow, and fungi on public restroom floors.

Pregnancy and birth

Review: The Influence of Early Infant-Feeding Practices on the Intestinal Microbiome and Body Composition in Infants – Aifric O’Sullivan – Nutrition and Metabolic Insights

Human oral microbiome

Review: Advances in the microbial etiology and pathogenesis of early childhood caries –
Evlambia Hajishengallis – Molecular Oral Microbiology

Human respiratory tract microbiome

Dead or alive: Deoxyribonuclease I sensitive bacteria and implications for the sinus microbiome – A.L. Williams – American Journal of Rhinology & Allergy

Human gut microbiome

Early life exercise may promote lasting brain and metabolic health through gut bacterial metabolites – Agnieszka Mika – Immunology & Cell Biology

Proton pump inhibitors alter the composition of the gut microbiota – Matthew A Jackson – Gut

Metagenomic Analysis Reveals Dynamic Changes of Whole Gut Microbiota in the Acute Phase of Intensive Care Unit Patients – Masahiro Ojima – Digestive Diseases and Sciences

Review: Dietary Emulsifiers, The Human Intestinal Mucus and Microbiome, and Dietary Fiber – Michael J. Glade – Nutrition

Review: Commensal bacteria modulate the tumor microenvironment – Theofilos Poutahidis – Cancer Letters

Review: Characterizing the Intestinal Microbiome in Infantile Colic. Findings Based on an Integrative Review of the Literature – Nancy E. Dubois – Biological Research For Nursing

Microbiome models

Variability in microbial population and fermentation traits at various sites within the forestomach and along the digestive tract as assessed in goats fed either grass or browse – J.O. Zeitz – Small Ruminant Research

Effect of roughage on rumen microbiota composition in the efficient feed converter and sturdy Indian Jaffrabadi buffalo (Bubalus bubalis) – Neelam M. Nathani – BMC Genomics

The Effect of Immigration on the Adaptation of Microbial Communities to Warming – Diane Lawrence – The American Naturalist

Animal microbiome

Birds: Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe – Zoë L. Grange – Microbial Ecology

More birds: Feather-degrading bacteria, uropygial gland size and feather quality in House Sparrows Passer domesticus – Attila Fülöp – Ibis

Plant, root, and soil microbiology

The Cultivable Surface Microbiota of the Brown Alga Ascophyllum nodosum is Enriched in Macroalgal-Polysaccharide-Degrading Bacteria – Marjolaine Martin – Frontiers in Microbiology

Characterization of Arbuscular Mycorrhizal Fungus Communities of Aquilaria crassna and Tectona grandis Roots and Soils in Thailand Plantations – Amornrat Chaiyasen – PLOS ONE

Water and extremophile microbiome

Characterization of Halophilic Bacterial Communities in Turda Salt Mine (Romania) – Rahela Carpa – Origins of Life and Evolution of Biospheres

Built environment microbiome

Rapid assemblage of diverse environmental fungal communities on public restroom floors – Jennifer Fouquier – Indoor Air

A simple novel device for air sampling by electrokinetic capture – Julian Gordon – Microbiome

Infection microbiology

Review: The biogeography of polymicrobial infection – Apollo Stacy – Nature Reviews Microbiology

Microbes in the news

Gut Microbiome Influenced by Early-Life Exercise – GenEngNews

Celebrating the good viruses of 2015 – Jason Tetro – Popular Science

End of the year lists

Science: Best long reads of 2015 (part one) – BBC

Science: Best long reads of 2015 (part two) – BBC

Science, publishing, and career

“Women Who Don’t Give a Crap” – Holly Tabor – PLOS Genetics

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December 24, 2015

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Merry Christmas! The stream of microbiome research papers never appears to take a break, so I will keep on posting during the holidays. Today I found two nice review papers on the oral microbiome and cystic fibrosis microbiome, an upcoming hands-on workshop on mothur (Microbial Ecology software), the acne microbiome, and bacterial exchange in your washing machine.

Events

Throughout the year, Pat offers 4-5 workshops on mothur and programming in R for microbial ecologists. February mothur workshop by Patrick Schloss, February 8-10, Detroit

General microbiome

Review: Tools for the Microbiome: Nano and Beyond – Julie S. Biteen – ACS Nano

Human skin microbiome

Microorganisms inhabiting follicular contents of facial acne are not only Propionibacterium but also Malassezia spp. – Narifumi Akaza – The Journal of Dermatology

Human oral microbiome

Review: Beyond the oral microbiome – Howard F. Jenkinson – Environmental Microbiology

Prevalence of Candida albicans and Candida dubliniensis in caries-free and caries-active children in relation to the oral microbiota—a clinical study – A. Al-Ahmad – Clinical Oral Investigations

Human respiratory microbiome

Looking beyond respiratory cultures: Microbiome-cytokine signatures of bacterial pneumonia and tracheobronchitis in lung transplant recipients – Jyoti Shankar – American Journal of Transplantation

The Lung Immune Response to Bacteria in Chronic Obstructive Pulmonary Disease – Paul T. King – American Journal of Respiratory and Critical Care Medicine

Review: The Microbiome in Cystic Fibrosis – Yvonne J. Huang – Clinics in Chest Medicine

Human gut microbiome

Not a very novel insight: Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing – Ravi Ranjan – Biochemical and Biophysical Research Communications

Review: The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota – Phillip A. Engen – Alcohol Research Current Reviews

Review: The First Line of Defense: The Effects of Alcohol on Post-Burn Intestinal Barrier, Immune Cells, and Microbiome – Adam M. Hammer

Microbiome models

Intestinal Microbiota Signatures Associated with Inflammation History in Mice Experiencing Recurring Colitis – David Berry – Frontiers in Microbiology

The Anti-Oxidant Drug Tempol Promotes Functional Metabolic Changes in the Gut Microbiota – Jingwei Cai – Journal of Proteome Research

Effects of the dietary protein level on the microbial composition and metabolomic profile in the hindgut of the pig – Liping Zhou – Anaerobe

Development of gut inflammation in mice colonized with mucosa-associated bacteria from patients with ulcerative colitis – Zhengyu Du – Gut Pathogens

Animal microbiome

The Metabolically Active Bacterial Microbiome of Tonsils and Mandibular Lymph Nodes of Slaughter Pigs – Evelyne Mann – Frontiers in Microbiology

Microbial community of Pacific abalone (Haliotis discus hannai) juveniles during a disease outbreak in South China – Liu-yang Shi – Aquaculture Research

The Role of Tissue-specific Microbiota in Initial Establishment Success of Pacific oysters – Ana Lokmer – Environmental Microbiology

Plant, root, and soil microbiomes

Impact of forest management practices on soil bacterial diversity and consequences for soil processes – Federica Colombo – Soil Biology and Biochemistry

Metagenomics study of endophytic bacteria in Aloe vera using next-generation technology – Mushafau Adewale Akinsanya – Genomics Data

Shifts of microbial community structure in soils of a photovoltaic plant observed using tag-encoded pyrosequencing of 16S rRNA – Shijin Wu – Applied Microbiology and Biotechnology

Copper pollution decreases the resistance of soil microbial community to subsequent dry–rewetting disturbance – Jing Li – Journal of Environmental Sciences

Switchgrass rhizospheres stimulate microbial biomass but deplete microbial necromass in agricultural soils of the upper Midwest, USA – Chao Liang – Soil Biology and Biochemistry

Water and waste microbiome

Occurrence and persistence of antibiotic resistance genes in river biofilms after wastewater inputs in small rivers – Lorenzo Proia – Environmental Pollution

Biogeochemical importance of the bacterial community in uranium waste deposited at Key Lake, Northern Saskatchewan – VF Bondici – Geomicrobiology Journal

Built environment microbiome

Bacterial Exchange in Household Washing Machines – Chris Callewaert- Frontiers in Microbiology

Survival of Antarctic Cryptoendolithic Fungi in Simulated Martian Conditions On Board the International Space Station – Onofri Silvano – Astrobiology

Darkening on lead-based pigments: Microbiological contribution – Tânia Rosado – Color Research & Application

Microbes in the news

Giant Balls of Bacteria Pile Up on Arctic Lake Beds, Ooze Toxin – Emily Benson – EOS

This Squid Could Help Humans Repel Dangerous Flesh-Eating Bacteria – Esther Inglis-Arkell – Gizmodo

Lackner Investigates Whether Brain Changes Affect Gut Microbiome – University of Buffalo

Science, publishing, and career

2015 London Naturejobs Career Expo: Science communication videos – Julie Gould – Nature Blogs
How to deal with the media
How to get a job
How to deal with articles that misrepresent science
Do you need a PhD?

Korean prosecutors seek jail time for professors in massive plagiarism scheme – Mark Zastrow – Retraction Watch

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December 23, 2015

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Dental plaque microbiota shifts during mechanic ventilation, different antibiotics have different effects in mice gut, the Tasmanian devil microbiome, supraglacial communities, and FISH visualization of bacteria.

Microbial detection from almost sterile sites

Absence of Bacteria on Coronary Angioplasty Balloons from Unselected Patients: Results with Use of a High Sensitivity Polymerase Chain Reaction Assay – Gorm Mørk Hansen – PLOS ONE

Pregnancy and birth microbiome

Editorial: Is there a link between viruses and necrotising enterocolitis? – Masako Shimamura – Acta Paediatrica

Human oral microbiome

Microbial profiling of dental plaque from mechanically ventilated patients – Kirsty M Sands – Journal of Medical Microbiology

Discovery and validation of potential bacterial biomarkers for lung cancer – Xinmin Yan – American Journal of Cancer Research

Human gut microbiome

Gut Microbiota Alterations can predict Hospitalizations in Cirrhosis Independent of Diabetes Mellitus – Jasmohan S. Bajaj – Scientific Reports

Editorial: Diarrhoea risk study underlines the difficulties in carrying out research in day care centre settings – Margareta Söderström – Acta Paediatrica

Review: Micromanagement in the gut: microenvironmental factors govern colon mucosal biofilm structure and functionality – Rosemarie De Weirdt – NPJ Biofilms and Microbiomes

Microbiome models

Antibiotic Treatment Affects Intestinal Permeability and Gut Microbial Composition in Wistar Rats Dependent on Antibiotic Class – Monica Vera-Lise Tulstrup – PLOS ONE

Spatial disturbances in altered mucosal and luminal gut viromes of diet-induced obese mice – Min-Soo Kim – Environmental Microbiology

Interaction of mouse splenocytes and macrophages with bacterial strains in vitro: the effect of age in the immune response – A.A. Van Beek – Beneficial Microbes

DGGE: Oral administration of kefiran exerts a bifidogenic effect on BALB/c mice intestinal microbiota – M.F. Hamet – Beneficial Microbes

A Spatially Continuous Model of Carbohydrate Digestion and Transport Processes in the Colon – Arun S. Moorthy – PLOS ONE

Beneficial metabolic effects of selected probiotics on diet-induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota – Jeanne Alard – Environmental Microbiology

Editorial: Gutsy Microbes Fly High in the Antiviral War – Javier Robalino – Trends in Microbiology

Animal microbiome

The Tasmanian devil microbiome—implications for conservation and management – Yuanyuan Cheng – Microbiome

Plant, root, and soil microbiome

Rock geochemistry induces stress and starvation responses in the bacterial proteome – Casey C. Bryce – Environmental Microbiology

Isolation, selection and evaluation of antagonistic yeasts and lactic acid bacteria against ochratoxigenic fungus Aspergillus westerdijkiae on coffee beans – G.V. de Melo Pereira – Letters in Applied Microbiology

Low multifunctional redundancy of soil fungal diversity at multiple scales – Akira S. Mori – Ecology Letters

Phosphorus depletion in forest soils shapes bacterial communities towards phosphorus recycling systems – Fabian Bergkemper – Environmental Microbiology

Comparison of bacterial and archaeal communities in depth-resolved zones in an LNAPL body – Maria Irianni-Renno – Applied Microbiology and Biotechnology

Water and extremophile microbiome

Supraglacial bacterial community structures vary across the Greenland ice sheet –
Karen A. Cameron – FEMS Microbiology Ecology

Identification of subannual patterns in microbial community signatures from individual sedimentary laminae using a freeze-coring approach – B. K. Harrison – Limnology and Oceanography

Respiratory quinones in Archaea: phylogenetic distribution and application as biomarkers in the marine environment – Felix J. Elling – Environmental Microbiology

Built environment microbiome

Review: Sources of airborne microorganisms in the built environment – Aaron J. Prussin II – Microbiome

Food microbiology

Abiotic Stress and Phyllosphere Bacteria Influence the Survival of Human Norovirus and Its Surrogates on Preharvest Leafy Greens – Malak A. Esseili – Applied and Environmental Microbiology

Microbiome of death

Microbial ecology of the salmon necrobiome: Evidence salmon carrion decomposition influences aquatic and terrestrial insect microbiomes – Jennifer L. Pechal – Environmental Microbiology

Metagenomics and bioinformatics

Identification and Resolution of Microdiversity through Metagenomic Sequencing of Parallel Consortia – William C. Nelson – Applied and Environmental Microbiology

Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes – Jiarong Guo – Applied and Environmental Microbiology

Techniques

MiL-FISH: Multilabeled Oligonucleotides for Fluorescence In Situ Hybridization Improve Visualization of Bacterial Cells – Mario P. Schimak – Applied and Environmental Microbiology

Microbes in the news

Salmonella traced to pet turtles is spreading once again – Helen Branswell – STAT news

Bacteria resistant to a “last resort” antibiotic have been found in the UK – Frida Garza – Quartz

Gene behavior distinguishes viral from bacterial infections – Laura Sanders – Science News

Near perfect balance in a microbiome paper – hopeful yet no hype – Jonathan Eisen – MicroBEnet

Beneficial bacteria in Hawaiian squid attracted to fatty acids – Phys.org

Conference update: Advances in Human Microbiome Science: Intestinal Diseases – The New York Academy of Sciences

Microbiology and art

Microbiology and Creative Extra Credit – Mark O. Martin – Microbes Rule
Science, publishing, and career

Diversity in Clinical and Biomedical Research: A Promise Yet to Be Fulfilled – Sam S. Oh – PLOS Medicine

Genome-editing revolution: My whirlwind year with CRISPR – Jennifer Doudna – Nature

Science and gender: Scientists must work harder on equality – Meg Urry – Nature

End of year lists

365 days: The science events that shaped 2015. Gene-editing, climate change and Pluto are among the year’s top stories – Monya Baker – Nature

The Coolest Science Stories You May Have Missed in 2015 – Jennifer Ouellette – Gizmodo
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December 22, 2015

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Periodontal disease associated with increased chance for breast cancer, rifaximin treatment of IBS patients, bacteria on surface of 2 different grape varieties in Spain, and a reproducible research workflow in R.

Human oral microbiome

Periodontal Disease and Breast Cancer: Prospective Cohort Study of Postmenopausal Women – Jo L. Freudenheim – Cancer Epidemiology, Biomarkers & Prevention

Distributions of Synergistetes in clinically-healthy and diseased periodontal and peri-implant niches – Xiao-Lin Yu – Microbial Pathogenesis

Human gut microbiome

Modulation of the gut microbiota composition by rifaximin in non-constipated irritable bowel syndrome patients: a molecular approach – Sara Soldi – Clinical and Experimental Gastroenterology

Roles of Sphincter of Oddi Laxity in Bile Duct Microenvironment in Patients with Cholangiolithiasis: From the Perspective of the Microbiome and Metabolome –
Tingbo Liang – Journal of the American College of Surgeons

Book chapter: Influence of Gut Microbiota on Hepatic Lipogenesis and Disease Pathogenesis – Vishal Singh – Hepatic De Novo Lipogenesis and Regulation of Metabolism

Review: Metabolic Interactions in the Gastrointestinal Tract (GIT): Host, Commensal, Probiotics, and Bacteriophage Influences – Luis Vitetta – MDPI Microorganisms

Book chapter: Gut Microbiome and Stress – Winnie-Pui-Pui Liew – Beneficial Microorganisms in Medical and Health Applications

Review: Dietary and Lifestyle Factors Associated with Colorectal Cancer Risk and Interactions with Microbiota: Fiber, Red or Processed Meat and Alcoholic Drinks – Tuan J. – GastroIntestinal Tumors

Models of microbiomes

Effect of chito-oligosaccharides over human faecal microbiota during fermentation in batch cultures – Inmaculada Mateos-Aparicio – Carbohydrate Polymers

Changes in gastric microbiota induced by Helicobacter pylori infection and preventive effects of Lactobacillus plantarum ZDY 2013 against such infection – Mingfang Pan – Journal of Dairy Science

Glycan:glycan interactions: High affinity biomolecular interactions that can mediate binding of pathogenic bacteria to host cells – Christopher J. Day – PNAS

Research highlight: A ‘fit’ microbiota to potentiate cancer immunotherapy – Maria Rescigno – Genome Medicine

Animal microbiome

Ecological Succession in the Honey Bee Gut: Shift in Lactobacillus Strain Dominance During Early Adult Development – Kirk E. Anderson – Host Microbe Interactions

A diverse array of new viral sequences identified in worldwide populations of the Asian citrus psyllid (Diaphorina citri) using viral metagenomics – Shahideh Nouri – Journal of Virology

Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia – Jamal S. M. Sabir – Science

Comparison of Fecal Microbial Communities between White and Black Pigs – Robin B. Guevarra – Journal of Applied Biological Chemistry

Plant, root, and soil microbiome

Bacterial diversity of Grenache and Carignan grape surface from different vineyards at Priorat wine region (Catalonia, Spain) – Maria del Carmen Portillo – International Journal of Food Microbiology

Field Application of the Mycorrhizal Fungus Rhizophagus irregularis Increases the Yield of Wheat Crop and Affects Soil Microbial Functionalities – Sanâa Wahbi – American Journal of Plant Sciences

Arbuscular mycorrhizal fungi reduced the ratios of inorganic/organic arsenic in rice grains – H. Li – Chemosphere

Characteristics of rhizosphere and bulk soil microbial communities in rubber plantations in Hainan Island, China – Wang, W. B. – Journal of Tropical Forest Science

Microbial community structure and its temporal changes in Rehmannia glutinosa rhizospheric soils monocultured for different years – Linkun Wu – European Journal of Soil Biology

Exotic Plant Alnus trabeculosa Alters the Composition and Diversity of Native Rhizosphere Bacterial Communities of Phragmites australis – Xueping Chen – Pedosphere

Long-term chronological shifts in bacterial communities and hydrolytic extracellular enzyme activities in the forty years following a land-use change from upland fields to paddy fields – Nan Jiang – Pedobiologia

Water microbiome

Resilience of SAR11 bacteria to rapid acidification in the high latitude open ocean – Manuela Hartmann – FEMS Microbiology Ecology

Selective pressure of temperature on competition and cross-feeding within denitrifying and fermentative microbial communities – Anna Hanke – Frontiers in Microbiology

Bioinformatics

Reproducible Research Workflow in R for the Analysis of Personalized Human Microbiome Data – Benjamin Callahan – Pacific Symposium on Biocomputing

Techniques

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys – William Walters – mSystems

Protocol: Studying Protistan Communities in Hydrocarbon-Contaminated Environments – Julia Johnke – Springer Protocols Handbooks

Microbes in the news

Harmful bacteria can survive in sandwich crackers, cookies for months, UGA study finds – Online Athens

Tomorrow’s Heart Drugs Might Target Gut Microbes – Ed Yong – The Atlantic

Bik’s Picks

Pharmacy delivery vans targeted by thieves seeking painkillers – David Armstrong – STAT news

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