Category Archives: Water microbiome

January 20, 2016

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Virome of children with diarrhea, bacterial communities in black truffles, arsenic biogeochemistry in an acid vapor-formed spring, distribution of microbes in microenvironments, and retraction of a PLOS ONE air microbiome paper.

Jobs and events

New job openings at Whole Biome: develops therapeutics and diagnostics targeting human microbiome, casual culture, and artisanal coffee

Human oral microbiome

Exploration of Human Salivary Microbiomes—Insights into the Novel Characteristics of Microbial Community Structure in Caries and Caries-Free Subjects – Jianye Zhou – PLOS ONE

Human respiratory microbiome

COPD is characterized by increased detection of Haemophilus influenzae, Streptococcus pneumoniae and a deficiency of Bacillus species – Jodie L. Simpson – Respirology

Human gut microbiome

The fecal virome of South and Central American children with diarrhea includes small circular DNA viral genomes of unknown origin – Tung Gia Phan – Archives of Virology

Perspective: Gut microbiota and aging – Paul W. O’Toole – Science

Review: Studies on Modulation of Gut Microbiota by Wine Polyphenols: From Isolated Cultures to Omic Approaches – Montserrat Dueñas – MDPI Antioxidants

Animal models

Postnatal Hematopoiesis and Gut Microbiota in NOD Mice Deviate from C57BL/6 Mice – Dina Silke Malling Damlund – Journal of Diabetes Research

Bacterial profile and bone healing in rats receiving cancer therapeutic doses of bisphosphonates and corticosteroids: a pilot study – Z. Jabbour – International Journal of Oral & Maxillofacial Surgery

Interaction between dietary lipids and gut microbiota regulates hepatic cholesterol metabolism – Robert Caesar – Journal of Lipid Research

Gut Microbiota Regulates K/BxN Autoimmune Arthritis through Follicular Helper T but Not Th17 Cells – Katharine E. Block – The Journal of Immunology

Editorial: Of Bugs and Drugs: How the Microbiome Controls Responsiveness to Antitumor Immunotherapy – Mandy L. Ford – American Journal of Transplantation

Animal microbiome

Most Low-Abundance “Background” Symbiodinium spp. Are Transitory and Have Minimal Functional Significance for Symbiotic Corals – Moo Joon Lee – Microbial Ecology

Isolation and assessment of gut bacteria from the Formosan subterranean termite, Coptotermes formosanus (Isoptera: Rhinotermitidae), for paratransgenesis research and application – Chinmay V. Tikhe – Insect Science

Plant, root, and soil microbiome

Black truffle: Temporal changes of bacterial communities in the Tuber melanosporum ectomycorrhizosphere during ascocarp development – Aurélie Deveau – Mycorrhiza

Isolation of N2-fixing rhizobacteria from Lolium perenne and evaluating their plant growth promoting traits – Antonio Castellano-Hinojosa – Journal of Basic Microbiology

Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees – J. B. Vincent – Molecular Ecology

Water, waste, and extremophile microbiome

Metagenome-scale analysis yields insights into the structure and function of microbial communities in a copper bioleaching heap – Xian Zhang – BMC Genetics

Microbial Community Structure and Arsenic Biogeochemistry in an Acid Vapor-Formed Spring in Tengchong Geothermal Area, China – Zhou Jiang – PLOS ONE

Phylogenetic conservation of freshwater lake habitat preference varies between abundant bacterioplankton phyla – Marian L. Schmidt – Environmental Microbiology

Food and cigarette microbiome

Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis – Robert E. Tyx – PLOS ONE

More microbes

Divorcing strain classification from species names – David Baltrus

Distributions of Virus-Like Particles and Prokaryotes within Microenvironments – Lisa M. Dann – PLOS ONE

Parallel Mapping of Antibiotic Resistance Alleles in Escherichia coli –
Sophie J. Weiss – PLOS ONE

Microbes in the news

Satire: Dung Beetle A Bit Fed Up With Diet – The Allium

How Climate Change Endangers Microbes–And Why That’s Not a Good Thing – Aspen T. Reese – Scientific American

CDC issues guidance to help monitor pregnant women for Zika virus – Helen Branswell – STATnews

Microbes and art

These Close-Up Shots Of Kitchen Mold Are Oddly Appealing: Nikita Teryoshin, Max Slobodda / Küchendienst – FastCoDesign

Science, publishing, and career

Here are the 10 — yes, 10 — reasons PLOS ONE retracted this paper (“Metagenomic Human Repiratory Air in a Hospital Environment”) – Shannon Palus – Retraction Watch

Ten easy ways you can support diversity in academia in 2016 – Jacquelyn Gyll – The Contemplative Mammoth

Bik’s Picks

When chickens go wild. The feral chickens of Kauai provide a unique opportunity to study what happens when domesticated animals escape and evolve – Ewen Callaway – Nature
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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 13, 2016

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Frozen vs fresh stool transplants, the primate skin microbiome, diet-induced extinctions, bacteria in breast milk from low income Mexican-American moms, and engineered poplar tree endosphere.

Events

Tapping the Human Microbiome (Kavli Hangout) – Tuesday, Jan. 19, 1:30 pm EST, with Janet Jansson, Rob Knight, and Jeff Miller

Pregnancy and birth microbiome

Bacterial microbiome of breast milk and child saliva from low-income Mexican-American women and children – Veronica Davé – Pediatric Research

Human vaginal microbiome

Review: Biotherapeutic agents and vaginal health – F. H. Al-Ghazzewi – Journal of Applied Microbiology

Human gut microbiome

Frozen vs Fresh Fecal Microbiota Transplantation and Clinical Resolution of Diarrhea in Patients With Recurrent Clostridium difficile Infection – Christine H. Lee – JAMA

Small Intestine Bacterial Overgrowth and Environmental Enteropathy in Bangladeshi Children – Jeffrey R. Donowitz – mBio

Animal and bioreactor models

Diet-induced extinctions in the gut microbiota compound over generations – Erica D. Sonnenburg – Nature

Intestinal epithelial TLR4 signaling affects epithelial function, colonic microbiota and promotes risk for transmissible colitis – Rishu Dheer – Infection and Immunity

Modulation of the human gut microbiota by dietary fibres occurs at the species level – Wing Sun Faith Chung – BMC Biology

Animal microbiome

Diversity and evolution of the primate skin microbiome – Sarah E. Council – Proceedings of the Royal Society B

Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification – N. S. Webster – Scientific Reports

Plant, root, and soil microbiome

Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome – Bram Beckers – PNAS

Invariant community structure of soil bacteria in subtropical coniferous and broadleaved forests – Xiaoli Wang – Scientific Reports

Food microbiology

Seasonal and Growth-Dependent Dynamics of Bacterial Community in Radish Sprouts – Hiroshi Asakura – Journal of Food Safety

Bacterial dynamics and metabolite changes in solid-state acetic acid fermentation of Shanxi aged vinegar – Sha Li – Applied Microbiology and Biotechnology

Transcriptomics

Functional Profiling of Unfamiliar Microbial Communities Using a Validated De Novo Assembly Metatranscriptome Pipeline – Mark Davids – PLOS ONE

Metagenomics and bioinformatics

Direct next-generation sequencing of virus-human mixed samples without pretreatment is favorable to recover virus genome – Dingchen Li – Biology Direct

Microbes in the news

DNA Genotek’s microbiome collection and stabilization blog – Lisa Gamwell – The Microbiome Snapshot

Human trials will test freeze-dried poop pills as a weight-loss treatment – David Nield – Science Alert

What is Zika virus? Interview with Derek Gatherer – Microbe Post

E. coli Slinky: Revealed: the awful anchor that lets urinary tract infections take hold – Josh Barney – University of Virginia

Bik’s Picks

Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces – Michael J. Ford – PLOS ONE

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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 11, 2016

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Bacteriome of bat flies, phyllosphere of Espeletia plants, microbial eukaryotes in a fjord, and decomposing human bodies.

Human gut microbiome

Editorial: Gut microbiota cool-down burning fat! The immune hypothesis – Remy Burcelin – Trends in Endocrinology & Metabolism

Animal models

The programming effects of nutrition-induced catch-up growth on gut microbiota and metabolic diseases in adult mice – Jia Zheng – Microbiology Open

Animal microbiome

The bacteriome of bat flies (Nycteribiidae) from the Malagasy region: a community shaped by host ecology, bacterial transmission mode, and host-vector specificity – David A Wilkinson – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Microbial and Functional Diversity within the Phyllosphere of Espeletia sp. in an Andean High Mountain Ecosystem – Carlos A. Ruiz-Pérez – Applied and Environmental Microbiology

Water and extremophile microbiome

Strong seasonality of marine microbial eukaryotes in a high-Arctic fjord (Isfjorden, West Spitsbergen) – Miriam Marquardt – Applied and Environmental Microbiology

Microbiome of death

Microbial Signatures of Cadaver Gravesoil During Decomposition – Sheree J. Finley – Microbial Ecology

Bioinformatics and metagenomics

Microvirga massiliensis sp. nov., the human commensal with the largest genome – Aurélia Caputo – Microbiology Open

Microbes in the news

Newborn Gut Bacteria Differs If Infants Breastfed Or Formula-Fed, Vaginal Or Cesarean Birthed – Tara Haelle – Forbes

Good Bacteria May Inhibit Growth Of Pathogen Causing Ear Infection And Pneumonia: Examples Of Food High In Good Bacteria – Katrina Pascual – Tech Times

College Town: WPI students literally get the dirt on bacteria-fighting viruses – Bonnie Russell – Telegram

Mark Zuckerberg’s Facebook post on vaccines sparks huge response – Ashley Welch – CBS News

Gates-backed NYC startup plumbs soil bacteria for tuberculosis therapy – Meghana Keshavan – MedCityNews

Living Bacteria Are Riding Earth’s Air Currents – Jim Morrison – Smithsonian

QIAGEN completed the acquisition of MO BIO Laboratories Inc – PR Newswire

Dirty Work: The Magic of Microbes with Sandor Katz – Matthew Zuras – Munchies

Why The Microbiome Is So Vital To Your Health – Josh Axe – Conscious Life News

What have the Romans ever done for us? Parasites in Europe and the Middle East during Roman Rule – Elisabeth Bik – microBEnet

Microbes and art

Microbial muses: Michele Banks talks about her microbial art – Nature Microbiology

Science, publishing, and career

Student Evaluations of Teaching (Mostly) Do Not Measure Teaching Effectiveness – Anne Boring – Science Open
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January 9, 2016

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Microbiomes of musk deer, Tasmanian Devils, Panamanian frogs, roots of truffle-associated Douglas firs, and the Great Barrier Reef lagoon.

General human microbiome

Editorial: Getting fat from an inflamed relationship? The revenge of the holobiont
Andrew Moore – BioEssays

Perspective: Has provoking microbiota aggression driven the obesity epidemic? – Benoit Chassaing – BioEssays

Pregnancy and birth

A Comparison of Three Bioinformatics Pipelines for the Analysis of Preterm Gut Microbiota using 16S rRNA Gene Sequencing Data – Erica Plummer- OMICS Proteomics & Bioinformatics

Review: Infection and preterm birth – Hugh C.G. Nadeau – Seminars in Fetal and Neonatal Medicine

Human gut microbiome

Gut Microbiota and Metabolic Endotoxemia in Young Obese Mexican Subjects – Radilla-Vázquez R.B. – Obesity Facts

Animal models

The Impact of Dietary Energy Intake Early in Life on the Colonic Microbiota of Adult Mice – Jinyu Xu – Scientific Reports

Western diet induces a shift in microbiota composition enhancing susceptibility to Adherent-Invasive E. coli infection and intestinal inflammation – Allison Agus – Scientific Reports

Resistant Starch Alters the Microbiota-Gut Brain Axis: Implications for Dietary Modulation of Behavior – Mark Lyte – PLOS ONE

Effects of BmCPV Infection on Silkworm Bombyx mori Intestinal Bacteria – Zhenli Sun – PLOS ONE

Antibiotic-treated versus germ-free rodents for microbiota transplantation studies – Randi Lundberg – Gut Microbes

Animal microbiome

The musk chemical composition and microbiota of Chinese forest musk deer males
Diyan Li – Scientific Reports

Pasteurellaceae bacteria from the oral cavity of Tasmanian Devils (Sarcophilus Harrisii) show high MIC values towards aminoglycosides and clindamycin – Nicole Gutman – Letters in Applied Microbiology

Skin bacterial diversity of Panamanian frogs is associated with host susceptibility and presence of Batrachochytrium dendrobatidis – Eria A Rebollar – The ISME Journal

Plant, root, and soil microbiome

Prokaryotic diversity in biodeteriorated wood coming from the Bükkábrány fossil forest – Katerina Nikolouli – International Biodeterioration & Biodegradation

Molecular screening of microbial communities for candidate indicators of multiple metal impacts in marine sediments from northern Australia – Alyssa Cornall – Environmental Toxicology and Chemistry

Characterizing root-associated fungal communities and soils of Douglas-fir (Pseudotsuga menziesii) stands that naturally produce Oregon white truffles (Tuber oregonense and Tuber gibbosum) – Gian Maria Niccolò Benucci – Mycorrhiza

Field degradation of aminopyralid and clopyralid and microbial community response to application in Alaskan soils – Patrick L. Tomco – Environmental Toxicology and Chemistry

Microbial community structure and predicted bacterial metabolic functions in biochar pellets aged in soil after 34 months – Daquan Sun – Applied Soil Ecology

Water and extremophile microbiome

Deep Microbial Life in High-Quality Granitic Groundwater from Geochemically and Geographically Distinct Underground Boreholes – Kohei Ino – Environmental Microbiology Reports

Low viral predation pressure in cold hypersaline Arctic sediments and limits on lytic replication – Jesse Colangelo-Lillis – Environmental Microbiology Reports

Metagenomic analysis suggests modern freshwater microbialites harbor a core and distinct microbial community – Richard A. White III – Frontiers in Microbiology

Partitioning of fungal assemblages across different marine habitats – T.C. Jeffries – Environmental Microbiology Reports

Impact of manufactured TiO2 nanoparticles on planktonic and sessile bacterial communities – Stéphane Jomini – Environmental Pollution

Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions – Hon Lun Wong – MDPI Microorganisms

Microbial genetic diversity in soils along salinealkaline gradients at the coast of Laizhou Bay – Feng Zhao – Protistology

Influence of Zinc on Bacterial Populations and their Proteolytic Enzyme Activities in Freshwater Environments: A Cross-Site Comparison – Lauren Rasmussen – Canadian Journal of Microbiology

Marine microbial communities of the Great Barrier Reef lagoon are influenced by riverine floodwaters and seasonal weather events – Florent E. Angly – Peer J

Food microbiology

Exploring the phenotypic space of non-Saccharomyces wine yeast biodiversity – Debra Rossouw – Food Microbiology

Infection microbiology

Oral Phage Therapy of Acute Bacterial Diarrhea With Two Coliphage Preparations: A Randomized Trial in Children From Bangladesh – Shafiqul Alam Sarker – EBioMedicine

Book Chapter: Reducing pathobiomes could slow arms race between man and microbes
S. Romano-Bertrand – Microbiology 5

Bioinformatics and metagenomics

Neptune: A Tool for Rapid Microbial Genomic Signature Discovery – Eric Marinier – BioRxiv

Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities – Lisa Oberding – MDPI Microorganisms

Conference abstracts from the 2015 IEEE International Conference onBioinformatics and Biomedicine (BIBM):
Leveraging the k-Nearest Neighbors classification algorithm for Microbial Source Tracking using a bacterial DNA fingerprint library – Jeffrey D McGovern
A computational framework for integrative analysis of large microbial genomics data – Erliang Zeng
Computational challenges in microbiome research – Mihai Pop

Microbes in the news

New Year’s Resolutions for your Microbiome – Anne Estes – Mostly Microbes

West Hartford Children Museum Starts Scientific Discussion Series – Kristin Stoller – Hartford Courant

Balbriggan pair named Young Scientists of the Year: Maria Louise Fufezan and Diana Bura claim first place for research into soil fertility and nematodes – Dick Ahlstrom – The Irish Times

Body’s bacteria don’t outnumber human cells so much after all – Tina Hesman Saey – Science News

Are we really made up of more bacteria than human cells? – Lindsey Kratochwill – Popular Science

P&G granted patent for prebiotic agent-containing composition targeting skin microbiome – Andrew McDougall – Cosmetic Design-Europe.com

Science, publishing, and career

Nobel winner pulls out of Melb conference run by controversial Indian company (OMICS, EB) – Andrew Masterson – The Age

Cheer up, my academic colleagues! We’re so lucky to do this job – Anonymous Academic – The Guardian

Publishers to require ORCID identifiers for authors – EurekAlert

Bik’s Picks

Healthy Diet Helps 183-Year-Old Tortoise Feel Young Again – Jason Bittel – National Geographic

 

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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