Category Archives: Human respiratory

January 29, 2016

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Prescription drugs and microbiome analyses, antimicrobial targets in sarcoidosis granulomas, host-microbiota interactions in antibiotic-associated diseases, and iridescence in self-organizing biofilms.

General microbiome

Perspective: Prescription drugs obscure microbiome analyses – Suzanne Devkota – Science

Review: The role of microbiota in cancer therapy – Ernesto Perez-Chanona – Current Opinion in Immunology

Human respiratory microbiome

COPD and the microbiome – Manoj J. Mammen – Respirology

Molecular Analysis of Sarcoidosis Granulomas Reveals Antimicrobial Targets – Joseph E Rotsinger – American Journal of Respiratory Cell and Molecular Biology

Human skin microbiome

Review: The microbiome and atopic eczema: More than skin deep – Charlotte L Thomas – Australasian Journal of Dermatology

Human gut microbiome

Gut microbiota and allergic disease in children – Sarah L. Bridgman – Annals of Allergy, Asthma & Immunology

Effects of enteral polymeric diet on gut microbiota in children with Crohn’s disease – Chloé Guinet-Charpentier – Gut

Review: Effect of antibiotics on gut microbiota, glucose metabolism and bodyweight regulation – a review of the literature – Kristian Hallundbæk Mikkelsen – Diabetes, Obesity and Metabolism

Animal models

Effects of dispersal limitation in the face of intense selection via dietary intervention on the faecal microbiota of rats – Heli J. Barron Pastor – Environmental Microbiology Reports

Fecal dysbiosis in miniature dachshunds with inflammatory colorectal polyps –
Hirotaka Igarashi – Research in Veterinary Science

Dietary antigens limit mucosal immunity by inducing regulatory T cells in the small intestine – Kwang Soon Kim – Science

Translocation of microbes and changes of immunocytes in the gut of rapid- and slow-progressor Chinese rhesus macaques infected with SIVmac239 – Lin-Tao Zhang – Immunology

From the Sonnenburg lab: Host-Microbiota Interactions in the Pathogenesis of Antibiotic-Associated Diseases – Joshua S. Lichtman – Cell Reports

Effect of Antimicrobial Consumption and Production Type on Antibacterial Resistance in the Bovine Respiratory and Digestive Tract – Boudewijn Catry – PLOS ONE

Animal microbiome

Symbiotic Bacteria in Gills and Guts of Chinese Mitten Crab (Eriocheir sinensis) Differ from the Free-Living Bacteria in Water – Meiling Zhang – PLOS ONE

Earthworm: Isolation, identification, and characterization of gut microflora of Perionyx excavatus collected from Midnapore, West Bengal – Tanushree Tulsian Samanta – Journal of Basic Microbiology

Plant, root, and soil microbiome

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction – Kiley W Seitz – The ISME Journal

Not a good paper (poor figures and language problems – see my comments on PubPeer), about carnivorous plant: Microbiome and Biocatalytic Bacteria in Monkey Cup (Nepenthes Pitcher) Digestive Fluid – Xin-Yue Chan – Scientific Reports

Microbial diversity drives multifunctionality in terrestrial ecosystems – Manuel Delgado-Baquerizo – Nature Communications

Various fungal communities colonise the functional wood tissues of old grapevines externally free from grapevine trunk disease symptoms – E. Bruez – Australian Journal of Grape and Wine Research

Arbuscular mycorrhizal fungi regulate soil respiration and its response to precipitation change in a semiarid steppe – Bingwei Zhang – Scientific Reports

Sewage sludge addition modifies soil microbial communities and plant performance depending on the sludge stabilization process – Eva Lloret – Applied Soil Ecology

Review: Engineering the Rhizosphere – Yves Dessaux – Trends in Plant Science

Water and extremophile microbiome

Bacterial diversity in the surface sediments of the hypoxic zone near the Changjiang Estuary and in the East China Sea – Qi Ye – Microbiology Open

Ecological succession reveals potential signatures of marine–terrestrial transition in salt marsh fungal communities – Francisco Dini-Andreote – The ISME Journal

Profiling microbial community in a watershed heavily contaminated by an active antimony (Sb) mine in Southwest China – Weimin Sun – Science of The Total Environment

More microbiology

A unique self-organization of bacterial sub-communities creates iridescence in Cellulophaga lytica colony biofilms – Betty Kientz – Scientific Reports

Bioinformatics and metagenomics

Ten Simple Rules for a Bioinformatics Journal Club – Andrew Lonsdale – PLOS Computational Biology

NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes – Gabriel A. Al-Ghalith – PLOS Computational Biology

Microbes in the news

Stop pooping! You’re killing sentient beings! – PZ Myers – Pharyngula

ASM’s Commitment to Interdisciplinary Microbiome Research – American Society for Microbiology

Fermentation Farm wants you to eat better bacteria – Kathleen Luppi – LA Times

This bacteria can live for years in distilled water, and causes abscess, seizures and death: Melioidosis / Burkholderia pseudomallei – Jacinta Bowler – Science Alert

Science, publishing, and career

How to read a scientific paper – Adam Ruben – Science

High rejection rates by journals ‘pointless’– Analysis suggests higher selectivity fails to increase journals’ impact factors – David Matthews – Times Higher Education

How to stop the sexual harassment of women in science: reboot the system – Zuleyka Zevallow – The Conversation

Bik’s Picks

Arthropods of the great indoors: characterizing diversity inside urban and suburban homes – Matthew A Bertone

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January 27, 2016

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Catching up after 2 busy days:

Effects of antibiotic use in Finnish children, skin microbiota of salmon transitioning from freshwater to seawater, and California coastal phages.

General human microbiome

Review: The microbial environment and its influence on asthma prevention in early life – Erika von Mutius – Journal of Allergy and Clinical Immunology

Human respiratory tract microbiome

COPD and the microbiome – Manoj J. Mammen – Respirology

Human urinary tract microbiome

Redefining Healthy Urine: A Cross-Sectional Exploratory Metagenomic Study of People With and Without Bladder Dysfunction – Suzanne L. Groah – The Journal of Urology

Human gut microbiome

Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children – Katri Korpela – Nature Communications

Animal models

Ingestion of Milk Containing Very Low Concentration of Antimicrobials: Longitudinal Effect on Fecal Microbiota Composition in Preweaned Calves – Richard Van Vleck Pereira – PLOS ONE

Editorial: Host response: Microbiota prime antiviral response – Julie K. Pfeiffer – Nature Microbiology

Animal microbiome

Comparison of Intestinal Microbiota in Intestinal Tracts of the Wild and Cultured Seahorses, Hippocampus trimaculatus (Leach) – Kai Wang – Journal of the World Aquaculture Society

Social wasps are a Saccharomyces mating nest – Irene Stefanini – PNAS

Transition from freshwater to seawater reshapes the skin-associated microbiota of Atlantic salmon – Jep Lokesh – Scientific Reports

The role of tissue-specific microbiota in initial establishment success of Pacific oysters – Ana Lokmer – Environmental Microbiology

Plant, soil, and root microbiome

Kisameet Clay Exhibits Potent Antibacterial Activity against the ESKAPE Pathogens – mBio

Plant-microbe communication enhances auxin biosynthesis by a root-associated bacterium Bacillus amyloliquefaciens SQR9 – Yunpeng Liu – Molecular Plant-Microbe Interactions

Individual-Based Model of Microbial Life on Hydrated Rough Soil Surfaces – Minsu Kim – PLOS ONE

Analysis of bacterial communities associated with potting media – A. M. Al‑Sadi – Springer Plus

Water microbiome

Persistence of F-Specific RNA Coliphages in Surface Waters from a Produce Production Region along the Central Coast of California – Subbarao V. Ravva – PLOS ONE

Built environment and waste microbiome

Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors – Igor Shuryak – PLOS ONE

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology – Łukasz Jałowiecki – PLOS ONE

Microbial Ecology

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

Predicting compositions of microbial communities from stoichiometric models with applications for the biogas process – Sabine Koch – Biotechnology for Biofuels

Microbes in the news

Early-Life Antibiotic Use Affects Gut Microbiome Composition, New Study Says – Genome Web

Classroom research project: detecting phages – MT Standard

 

Uncovering hidden microbial lineages from hot springs – EurekAlert

Your Food’s Bacteria is a Big Data Gold Mine. IBM and Mars are tracking food’s microbiome to improve safety and productivity – David Z. Morris – Fortune

What Causes Cavities? The Balance Of Bacteria In Your Mouth Can Lead To Tooth Decay – Samantha Olson – Medical Daily

First Nations’ ancient medicinal clay shows promise against today’s worst bacterial infections – University of British Columbia

Ferring, Karolinska Institutet Launch Human Microbiome Collaboration – GenEngNews

WTF?: Fat Summit conference: Deepak Chopra Says Bacteria Listen To Our Thoughts – “we are the awakening of bacterial consciousness” – Kavin Senapathy – Forbes
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January 22, 2016

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Viruses in desert soils, pneumonia etiology, and a concerning editorial in NEJM.

Human oral microbiome

Microbiological analysis after complete or partial removal of carious dentin using two different techniques in primary teeth: A randomized clinical trial – Deepak Kumar Singhal – Dental Research Journal

Human respiratory microbiome

The Modern Quest for the “Holy Grail” of Pneumonia Etiology – Seema Jain – Clinical Infectious Diseases

Plant, root, and soil microbiome

Review: Diversity and Ecology of Viruses in Hyperarid Desert Soils – Olivier Zablocki – Applied and Environmental Microbiology

Use of Substrate-Induced Gene Expression in Metagenomic Analysis of an Aromatic Hydrocarbon-Contaminated Soil – Matthew J. Meier – Applied and Environmental Microbiology

Techniques / phages and viruses

Isolation of Polyvalent Bacteriophages by Sequential Multiple-Host Approaches – Pingfeng Yu – Applied and Environmental Microbiology

More microbiology

Tuberculosis in Newborns: The Lessons of the “Lübeck Disaster” (1929–1933) – Gregory J. Fox – PLOS Pathogens

Microbes in the news

For children: Understanding Marine Microbes, the Driving Engines of the Ocean – Anna Kopf

15 min podcast: A Microbiome Is Born – Science Friday

Good Bacteria for Good Skin – Beauty brands say there is a beneficial effect when probiotics and fermented ingredients are applied topically – Fiorella Valdesolo – Wall Street Journal

Your DNA could make you resistant to certain bacteria – gene expression could help explain why some people are more immune to infection than others – Alexandra Ossola – Popular Science

Science, publishing, and career

An editorial in NEJM called Data Sharing, written by Dan L. Longo and Jeffrey M. Drazen, caused a lot of concern because it calls scientists who use other people’s published data “parasites”. Some reactions:

Data Scientists = Research Parasites? – David Shaywitz – Forbes

Research “parasitism” and authorship rights – Leonid Schneider – For Better Science

Attack of the Research Parasites – Derek Lowe – Science Magazine blogs

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January 21, 2016

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Beards and MRSA in hospital workers, dysbiosis in Crohns Disease, non-absorbable antibiotics affect offspring in mice, bacterial sunscreens, and bacteria found in a sick-making building.

Events

2nd Annual Microbiome Symposium – January 25, 2016 – Stanford University, Palo Alto, CA

Pregnancy and birth

A necrotizing enterocolitis-associated gut microbiota is already present in the meconium: results of a prospective study – Fardou H. Heida – Clinical Infectious Diseases

Human oral microbiome

Salivary pathogen and serum antibody to assess the progression of chronic periodontitis: a 24-mo prospective multicenter cohort study – T. Morozumi – Journal of Periodontal Research

Human skin microbiome

Bacterial ecology of hospital workers’ facial hair: a cross-sectional study – E. Wakeam – Journal of hospital infection

Human respiratory microbiome

Correlation of the lung microbiota with metabolic profiles in bronchoalveolar lavage fluid in HIV infection – Sushma K. Cribbs – Microbiome

Human gut microbiome

Changes in Colonic Bile Acid Composition following Fecal Microbiota Transplantation Are Sufficient to Control Clostridium difficile Germination and Growth – Alexa R. Weingarden – PLOS ONE

Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn’s Disease – Takahashi K – Digestion

Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota – Feng Wang – Cell Reports

DNA fingerprinting approaches to trace Escherichia coli sharing between dogs and owners  – Z. Naziri – Journal of Applied Microbiology

Altered intestinal microbiota as a major driving force in alcoholic steatohepatitis – Herbert Tilg – Gut

Impact of Surotomycin on the Gut Microbiota of Healthy Volunteers in a Phase 1 Clinical Trial – Diane M. Citron – Antimicrobial Agents and Chemotherapy

Microbiome animal and bioreactor models

Administration of Non-Absorbable Antibiotics to Pregnant Mice to Perturb the Maternal Gut Microbiota Is Associated with Alterations in Offspring Behavior – Shiro Tochitani – PLOS ONE

Degradation of chondroitin sulfate by the gut microbiota of Chinese individuals –
Qingsen Shang – International Journal of Biological Macromolecules

Streptococcus pneumoniae colonization disrupts the microbial community within the upper respiratory tract of aging mice – Netusha Thevaranjan – Infection and Immunity

Assessing microbial competition in a hydrogen-based membrane biofilm reactor (MBfR) using multidimensional modeling – Kelly J. Martin – Biotechnology and Bioengineering

Animal microbiome

Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs – Pedro R. Frade – PLOS ONE

Plant, root, and soil microbiome

Bacteria increase arid-land soil surface temperature through the production of sunscreens – Estelle Couradeau – Nature Communications

Historical and current climate drive spatial and temporal patterns in fungal endophyte diversity – Hannah Giauque – Fungal Ecology

Location, location, location: priority effects in wood decay communities may vary between sites – Jennifer Hiscox – Environmental Microbiology

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation – Matthew T. Agler – PLOS Biology

Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils – José A. Siles – FEMS Microbiology Ecology

Effects of manure and mineral fertilization strategies on soil antibiotic resistance gene levels and microbial community in a paddy–upland rotation system – Hui Lin – Environmental Pollution

Bacterial community compositions in sediment polluted by perfluoroalkyl acids (PFAAs) using Illumina high-throughput sequencing – Yajun Sun – Environmental Science and Pollution Research

Large amounts of easily decomposable carbon stored in subtropical forest subsoil is associated with r-strategy-dominated soil microbes – Yuping Chen – Soil Biology and Biochemistry

Water, waste, and extremophile microbiome

Effects of anthropogenic heavy metal contamination on litter decomposition in streams – A meta-analysis – Verónica Ferreira – Environmental Pollution

Investigation of the microbial community in the Odisha hot spring cluster based on the cultivation independent approach – Archana Singh – Genomics Data

Analysis of bacterial diversity in two oil blocks from two low-permeability reservoirs with high salinities – Meng Xiao – Scientific Reports

Occurrence of mycotoxins and yeasts and moulds identification in corn silages in tropical climate – B.F. Carvalho – Journal of Applied Microbiology

Food microbiology

Molecular diversity of bacteria in commercially available ‘‘Spirulina’’ food supplements – Elisabeth Vardaka – PeerJ

Ineffective hand washing and the contamination of carrots after using a field latrine – J M Monaghan – Letters in Applied Microbiology

Microbiological characterization using combined culture dependent and independent approaches of Casizolu pasta filata cheese – N.P. Mangia – Journal of Applied Microbiology

Microbial dynamics in mixed culture biofilms of bacteria surviving sanitation of conveyor belts in salmon-processing plants – S. Langsrud – Journal of Applied Microbiology

Built environment microbiology

Bacteria in a water-damaged building: associations of actinomycetes and non-tuberculous mycobacteria with respiratory health in occupants – J.-H. Park – Indoor Air

Bioinformatics and metagenomics

Review: Application of multivariate statistical techniques in microbial ecology – O. Paliy – Molecular Ecology

More microbiology

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

Review: Within-host evolution of bacterial pathogens – Xavier Didelot – Nature Reviews Microbiology

This is NOT novel and methods are missing essential steps: A novel method to assess the biodiversity of parasites using 18S rDNA Illumina sequencing; parasitome analysis method – Akina Hino – Parasitology International

Microbes in the news

Found: Desert Hot Spots Just For Microbes – Sarah Laskow – Atlas Obscura

Beards may be more hygienic and bacteria-resistant than shaven skin, study finds – Kate Ng – Independent
Beards may not be that gross, after all – Rachel Thompson – Mashable
Are beards good for your health? – BBC News Magazine

Bacteria or virus? New diagnostic tool could curb antibiotic overuse – Eric Boodman – STAT news

Getting to know the real you – how seriously should we take the health of our internal aliens? – LabNews UK

Probiotics come with bold health claims, but the science is shaky – Megan Scudellari – STAT news

Weekend binges just as bad for the gut as a regular junk food diet, study suggests – Dan Wheelahan – Medical Xpress

Can our gut microbiota contribute to the effect healthy foods have on us? – Gut Microbiota WorldWatch

Science, publishing, and career

Are results in top journals to be trusted? – SK – Economist

The best academic acknowledgements ever – Glen Wright – Times Higher Education
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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 4, 2016

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Human respiratory microbiome

Review: Cystic Fibrosis Lung Infections: Polymicrobial, Complex, and Hard to Treat – Laura M. Filkins – PLOS Pathogens

Human gut microbiome

Special issue: Obesity, Cancer and Nutrition, Gut Microbiota – Hans-Ulrich Humpf – Molecular Nutrition & Food Research

Plant, root, and soil microbiome

The microbiome of the leaf surface of Arabidopsis protects against a fungal pathogen – Unyarat Ritpitakphong – New Phytologist

Water microbiome

Bacterial communities and their association with the bio-drying of sewage sludge – Lu Cai – Water Research

Microbes in the news

Germs for the holidays: House guests leave trail of tiny, immunity-improving bacteria – Jo Napolitano – UChicago News

Gut bacteria differ when zinc goes missing – Krishna Ramanujan – Futurity

Milwaukee harbor a ‘hot spot’ for bacteria resistant to antibiotics – Don Behm – Journal Sentinel

Disturbances to infant microbiota influences disease risk, scientists find – Donald Acosta – International Business Times

Shocking bacteria out of their safety zone – Mohit M. Rao – The Hindu

More than you ever wanted to know about dung beetles – Jason Bittel – Earth Touch News

Methane-guzzling bacteria could feed fish, pets, even people – Digesting waste gas from garbage dumps could help save the planet, too – Kim Brunhuber – CBC news

Science, publishing, and career

Christie Fowler: Addicted to Research. Assistant Professor, Department of Neurobiology and Behavior University of California, Irvine. Age: 39 – Kerry Grens – The Scientist

The illusion of self-correction – Ferric Fang and Arturo Casadevall – Chemistry World

Can’t Disrupt This: Elsevier and the 25.2 Billion Dollar A Year Academic Publishing Business – Jason Schmitt – SAS Confidential

Wild Card Career Choice Becomes My Trump Card: “Not pathology. You’ll be wearing Wellies and sluicing down body parts in a morgue. You’ll never get a boyfriend that way.” – Sarah Thomas – Huffington Post

The Incredible Thing We Do During Conversations. When we take turns speaking, we chime in after a culturally universal short gap – Ed Yong – The Atlantic

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January 2, 2016

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Sinus communities in rhinosinusitis patients, arsenic metabolism genes in paddy soils, and a review on Metagenomic Chromosome Conformation Capture.

Pregnancy and birth

Human Milk Bacterial and Glycosylation Patterns Differ by Delivery Mode – Marina Hoashi – Reproductive Sciences

Human respiratory microbiome

Bacterial communities vary between sinuses in chronic rhinosinusitis patients – Tom V. Joss – Frontiers in Microbiology

Review with some plagiarized text: Potential of Microbiome Research in Respiratory Diseases – Prakash S. Bisen – Journal of Respiratory Research

Plant, root, and soil microbiome

Metagenomic analysis revealed highly diverse microbial arsenic metabolism genes in paddy soils with low-arsenic contents – Ke-Qing Xiao – Environmental Pollution

Evaluating the diversity of soil microbial communities in vineyards relative to adjacent native ecosystems – Taylor C. Holland – Applied Soil Ecology

Life at the interface: above- and below-ground responses of a grazed pasture soil to reforestation – T.R. Cavagnaro – Applied Soil Ecology

Water and waste microbiome

Antibiotic Resistance Genes and Human Bacterial Pathogens: Co-occurrence, Removal, and Enrichment in Municipal Sewage Sludge Digesters – Feng Ju – Water Research

Impacts of reclaimed water irrigation on soil antibiotic resistome in urban parks of Victoria, Australia – Xue-Mei Han – Environmental Pollution

Extremophile microbiome

Recombination does not hinder formation or detection of ecological species of Synechococcus inhabiting a hot spring cyanobacterial mat – Melanie C. Melendrez – Frontiers in Microbiology

Bioinformatics and metagenomics

Pathosphere.org: pathogen detection and characterization through a web-based, open source informatics platform – Andy Kilianski – BMC Bioinformatics

Review, awaiting peer review: Metagenomic Chromosome Conformation Capture (3C): techniques, applications, and challenges – Michael Liu – F1000 Research

Conference abstract: Time series analysis of microbiome data regularized by local linear manifold – Xingpeng Jiang – 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Conference abstract: A novel dimensionality reduction algorithm based on Laplace matrix for microbiome data analysis – Yetian Fan – 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Microbes in the news

New studies show dirty humidifiers grow bacteria that can lead to sickness – Candy Johansen – Inquisitr

Consumer Reports: Bacteria-Breeding Humidifiers – Sarah Arbogast – CBS Pittsburg

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January 1, 2016

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Happy New Year to you all. We’ll start the year off with a nice graph made by Jonathan Eisen, showing how the microbiome literature has been growing in the past 10 years:

Screen Shot 2016-01-01 at 2.11.23 PM

It’s hard to keep up sometimes with all those new papers, but I will do my best for you all in the new year. The year is not even one day old, and already 154 papers were published in 2016, so it’s going to be a very busy year! Here is a plot I made on the papers published since 2000 to illustrate.

Microbiome Pubmed 2015

Today’s digest features the microbiomes from different Mongolian and Indian tribes.

Pregnancy and birth

Safety, growth, and support to healthy gut microbiota by an infant formula enriched with functional compounds – Elisa Civardi – Clinical Nutrition

Human respiratory microbiome

Alteration in Bacterial Culture After Treatment With Topical Mupirocin for Recalcitrant Chronic Rhinosinusitis – Tara F. Carr – JAMA Otolaryngology – Head & Neck Surgery

Human gut microbiome

Gut bacterial diversity of the tribes of India and comparison with the worldwide data – Madhusmita Dehingia – Scientific Reports

Faecal microbiome in new-onset juvenile idiopathic arthritis – M. V. Tejesvi – European Journal of Clinical Microbiology & Infectious Diseases

No good direct link: Lost in Translation: The Gut Microbiota in Psychiatric Illness – Rebecca Anglin – Canadian Journal of Psychiatry

Water microbiome

Cable Bacteria Control Iron-Phosphorus Dynamics in Sediments of a Coastal Hypoxic Basin – Fatimah Sulu-Gambari- Environmental Science & Technology

Microbes in the news

The U.S. Army wants you—to eat MREs for 3 weeks, conducting a study on how ”Meals, ready-to-eat” affect gut health – Kristin Toussaint- Boston

Microbiomania and Fecal Transplants – Jonathan Eisen – The Tree Of Life

Are Antibiotics Safe for Children: 4 Risks of Antibiotic Overuse – Chelsea Clark – Mother Earth News

Clearing Gut Infections – A look at how phage therapy differs from antibiotic treatment – Jyoti Madhusoodanan – The Scientist

Woods Hole Scientist Amy Apprill Featured In Science Magazine Video Series – Andrea F. Carter – CapeNews

Exercising early changes gut microbes for the better – Tim Sandle – Digital Journal

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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 29, 2015

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Human respiratory microbiome

Culture-based and culture-independent bacteriologic analysis of cystic fibrosis respiratory specimens – Mona A. Mahboubi – Journal of Clinical Microbiology

Human gut microbiome

Review: Could the Gut Microbiota Reconcile the Oral Bioavailability Conundrum of Traditional Herbs? – Feng Chen – Journal of Ethnopharmacology

Chapter: Antimicrobial Peptides in the Gut – Maureen J. Ostaff – Antimicrobial Peptides

Review: Commensal ‘trail of bread crumbs’ provide pathogens with a map to the intestinal landscape – Deborah H Luzader – Current Opinion in Microbiology

Review: New frontiers in nanotoxicology: Gut microbiota/microbiome-mediated effects of engineered nanomaterials – Antonio Pietroiusti – Toxicology and Applied Pharmacology

Review: Nonalcoholic Fatty Liver Disease and the Gut Microbiome – Jerome Boursier – Clinics in Liver Disease

Review: Beneficial Microbes: The pharmacy in the gut – Daniel M. Linares – Bioengineered

Microbiome models

Selective Spectrum Antibiotic Modulation of the Gut Microbiome in Obesity and Diabetes Rodent Models – Deepak K. Rajpal – PLOS ONE

Animal microbiome

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

Plant, root, and soil microbiome

Experimental Evidence that Fungi are Dominant Microbes in Carbon Content and Growth Response to Added Soluble Organic Carbon in Moss-rich Tundra Soil – O. Roger Anderson – The Journal of Eukaryotic Microbiology

Relative Roles of Deterministic and Stochastic Processes in Driving the Vertical Distribution of Bacterial Communities in a Permafrost Core from the Qinghai-Tibet Plateau, China – Weigang Hu – PLOS ONE

Legacy effects of soil moisture on microbial community structure and N2O emissions – Samiran Banerjee – Soil Biology and Biochemistry

Water microbiome

High concentrations of bioavailable heavy metals impact freshwater sediment microbial communities – Caiying Ni – Annals of Microbiology

Techniques

Enhanced sequencing coverage with digital droplet multiple displacement amplification – Angus M. Sidore – Nucleic Acids Research

BioDry: An Inexpensive, Low-Power Method to Preserve Aquatic Microbial Biomass at Room Temperature – Steven J. Tuorto – PLOS ONE

Review: The A, C, G, T of Genome Assembly – Bilal Wajid – BioMed Research International

More Microbiology

Microbiology: A division of labour combined – Marcel M. M. Kuypers – Nature

PhD Thesis: Bacterial Predation in Host Microbiomes – Welsh, Rory M. – Oregon State

Microbes in the news

It’s Hard to Poop on Vacation – Why the holidays are a prime time for traveler’s constipation – Mollie Bloudoff-Indelicato – The Atlantic

Referring to a review based on debatable research: Babies in the Womb Aren’t So Sterile After All – Alice Park – Time

New Studies Suggest Microorganisms in the Womb Set Stage For Childhood and Adulthood Diseases – PR Web

Officials Expand Quarantine In Calif. To Battle Bug That Carries Bacteria Fatal To Citrus Trees – CBS Sacramento

Book reviews: ‘The Diet Myth,’ ‘The Good Gut’ and ‘The Hidden Half of Nature’ – Sonia Shah – The New York Times

http://news.co.cr/bacteria-from-antarctica-could-be-used-in-cancer-treatment/43621/Bacteria from Antarctica Could be Used in Cancer Treatment – Costa Rica Star

Activist Christopher Swain swims in ‘toilet bowl of bacteria’ – Scott Enman – Brooklyn Daily Eagle

Letters: We need a new strategy in the war against bacteria – The Independent
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