Category Archives: Pregnancy and birth

January 24, 2016

Posted on by

Antibiotic therapy in preterm labor, shrimp microbial dynamics, volcanic desert on Mount Fuji, coffee processing, and Antarctic permafrost limits microbial life.

Pregnancy and birth

Antibiotic Therapy Increases the Risk of Preterm Birth in Preterm Labor without Intra-Amniotic Microbes, but may Prolong the Gestation Period in Preterm Labor with Microbes, Evaluated by Rapid and High-Sensitive PCR System – Satoshi Yoneda – American Journal of Reproductive Immunology

Human gut microbiome

Does the Intestinal Microbiota Explain Differences in the Epidemiology of Liver Disease between East and West – Nakamoto N. – Inflammatory Intestinal Diseases

Commentary: Microbiome-based companion diagnostics: no longer science fiction?
Jeroen Raes – Gut

Animal microbiome

Diary of a shrimpy kid: Dynamic changes of microbial communities in Litopenaeus vannamei cultures and the effects of environmental factors – Hao Zhang – Aquaculture

Plant, root, and soil microbiome
Substrate limitation to soil microbial communities in a subalpine volcanic desert on Mount Fuji, Japan – S. Yoshitake – European Journal of Soil Biology

Bottom-up control of fertilization on soil nematode communities differs between crop management regimes – Ting Liu – Soil Biology and Biochemistry

Interactive effects of precipitation and nitrogen spatial pattern on carbon use and functional diversity in soil microbial communities – Nianxun Xi – Applied Soil Ecology

Water and extremophile microbiome

Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica – Jacqueline Goordial – The ISME Journal

Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments – Petter Thureborn – PeerJ

 

Waste treatment microbiology

Metagenomic and quantitative insights into microbial communities and functional genes of nitrogen and iron cycling in twelve wastewater treatment systems – Duntao Shu – Chemical Engineering Journal

Food microbiology

High throughput sequencing identifies novel viruses in nectarine: Insights to the etiology of stem pitting disease – Dan Edward Veloso Villamor – Phytopathology

DGGE: Discrimination of post-harvest coffee processing methods by microbial ecology analyses – Yasmine Hamdouche – Food Control

Microbial Ecology

Integrating Theory and Experiment to Explain the Breakdown of Population Synchrony in a Complex Microbial Community – Emma J. Bowen – arXiv

Techniques

Poster abstract: Assembling Whole Genomes from Mixed Microbial Communities Using Hi-C – Ivan Liachko – Plant and Animal Genome Conference

Microbes in the news

Antarctic permafrost may not be habitable for microbes – so is Mars? Finding life on Mars might be harder than thought — or Martian microbes might be different – Emily Chung – CBC News

Microbes take their vitamins — for the good of science – EurekAlert

Bacteria that resist last-resort antibiotics were found in China two months ago, now they’re everywhere – Dominic Jackson – Shanghaiist

Newly Discovered Photosynthetic Bacteria Is Surprisingly Abundant – Science 2.0

[hr]

January 21, 2016

Posted on by

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
[hr]

January 12, 2016

Posted on by

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
[hr]

January 9, 2016

Posted on by

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

Posted on by

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
[hr]

January 7, 2016

Posted on by

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
[hr]

January 5, 2016

Posted on by

Bacteria in breastmilk, nose/skin bacteria preventing pneumococcal infection, biofilms on pig carcasses in flowing water, Jurassic microbial mats, and Comammox Nitrospira-like bacteria in drinking water.

Pregnancy and birth

Characterization of bacterial isolates from the microbiota of mothers’ breast milk and their infants – Kimberly Kozak – Gut Microbes

Review: Association Between the Gut Microbiota and Diet: Fetal Life, Early Childhood, and Further Life – D.A. Kashtanova – Nutrition

Human nose/skin microbiome

Corynebacterium accolens Releases Antipneumococcal Free Fatty Acids from Human Nostril and Skin Surface Triacylglycerols – Lindsey Bomar – mBio

Human gut microbiome

A dysbiotic subpopulation of alcohol-dependent subjects – Philippe de Timary – Gut Microbes

Colorectal cancer: role of commensal bacteria and bystander effects – Xingmin Wang – Gut Microbes

Review: Gut inflammation and microbiome in spondyloarthritis – Jayakanthan Kabeerdoss – Rheumatology International

Review: Gut Microbiota and Celiac Disease – Giovanni Marasco – Digestive Diseases and Sciences

Animal models

Pglyrp-Regulated Gut Microflora Prevotella falsenii, Parabacteroides distasonis and Bacteroides eggerthii Enhance and Alistipes finegoldii Attenuates Colitis in Mice – Roman Dziarski – PLOS ONE

Plant, root, and soil microbiome

Dynamics of viral abundance and diversity in a Sphagnum-dominated peatland: temporal fluctuations prevail over habitat – Flore C. Ballaud – Frontiers in Microbiology

Distribution of Root-Associated Bacterial Communities Along a Salt-Marsh Primary Succession – Miao Wang – Frontiers in Plant Science

Early Jurassic microbial mats – a potential response to reduced biotic activity in the aftermath of the end-Triassic mass extinction event – Olof Peterffy – Palaeogeography, Palaeoclimatology, Palaeoecology

Water and extremophile microbiome

Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals – Jennifer M. Lang – Microorganisms

Effect of water chemistry on zooplanktonic and microbial communities across freshwater ecotones in different macrophyte-dominated shallow lakes – Tomasz Mieczan – Journal of Limnology

Influences of microbial communities on groundwater component concentrations during managed artificial recharge – Wenjing Zhang – Environmental Earth Sciences

Complete metagenome sequencing based microbial diversity insights from Deccan basaltic hot spring of Unkeshwar, Maharashtra, India – Gajanan T. Mehetre – Genomics Data

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

Built environment and waste microbiome

Metagenomic Evidence for the Presence of Comammox Nitrospira-Like Bacteria in a Drinking Water System – Ameet J. Pinto – mSphere

Proteolytic bacterial dominance in a full-scale municipal solid waste anaerobic reactor assessed by 454 pyrosequencing technology – Juliana Cardinali-Rezende – Chemosphere

Food microbiology

Microbial dynamics during shelf-life of industrial Ricotta cheese and identification of a Bacillus strain as a cause of a pink discolouration – E. Sattin – Food Microbiology

Microbes in the news

Outbreaks of Salmonellosis from Small Turtles – Maroya Spalding Walters – Pediatrics

Many of these are amazing because of microbes: 17 of the world’s weirdest water features – Marnie Hunter – CNN

Study details how good bacteria might help prevent middle ear infections and pneumonia – EurekAlert

Study: Bacteria, electrons spin in similar patterns. Bacteria streaming through a lattice behave like electrons in a magnetic material – EurekAlert
[hr]

December 31, 2015

Posted on by

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

[hr]

December 26, 2015

Posted on by

Gut microbiota of patients with and without abdominal bloating, probiotics to help with academic stress, and a copper gradient near a Canadian mine.

Pregnancy and birth

Review: The microbiome and childhood diseases: Focus on brain-gut axis –
Siobhain M. O’ Mahony – Birth Defects Research Part C: Embryo Today: Reviews

Human respiratory tract microbiome

Microbiological and Molecular Identification of Bacterial Species Isolated from Nasal and Oropharyngeal mucosa of Fuel Workers in Riyadh, Saudi Arabia – Suaad S. AlWakeel – Saudi Journal of Biological Sciences

Human gut microbiome

Molecular Characterization of the Intestinal Microbiota in Patients With and Without Abdominal Bloating – Tamar Ringel-Kulka – American Journal of Physiology

Microbiome models

Choline Diet and Its Gut Microbe–Derived Metabolite, Trimethylamine N-Oxide, Exacerbate Pressure Overload–Induced Heart Failure – Chelsea L. Organ – Circulation: Heart Failure

Bidirectional interactions between indomethacin and the murine intestinal microbiota
Xue Liang

A simple coculture system shows mutualism between anaerobic faecalibacteria and epithelial Caco-2 cells – Mehdi Sadaghian Sadabad – Scientific Reports

Animal microbiome

Metagenomic assessment of the functional potential of the rumen microbiome in Holstein dairy cows – Dipti W. Pitta – Anaerobe

Age-Related Shifts in Bacterial Diversity in a Reef Coral – Alex D. Williams – PLOS ONE

Microbial composition of biofilms associated with lithifying rubble of Acropora palmata branches – Yislem Beltrán – FEMS Microbiology Ecology

Plant, root, and soil microbiome

Comparisons of diazotrophic communities in native and agricultural desert ecosystems reveal plants as important drivers in diversity – Martina Köberl – FEMS Microbiology Ecology

Locally adapted arbuscular mycorrhizal fungi improve vigor and resistance to herbivory of native prairie plant species – Elizabeth L. Middleton – Ecosphere

Root Exudation by Aphid Leaf Infestation Recruits Root-associated Paenibacillus spp. to Lead Plant Insect Susceptibility – Bora Kim – Journal of Microbiology and Biotechnology

Effects of the allelochemical coumarin on plants and soil microbial community – E. Niro – Soil Biology and Biochemistry

Water and waste microbiome

Microbiome analysis across a natural copper gradient at a proposed Northern Canadian mine site – Thea Van Rossum – Frontiers in Environmental Science

Evaluation of Community-Level Physiological Profiling for Monitoring Microbial Community Function in Aquaculture Ponds – Gerald L. Kurten – North American Journal of Aquaculture

Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages – David H. Case – mBio

Microbial colonisation and litter decomposition in a Cerrado stream are limited by low dissolved nutrient concentrations – Adriana O. Medeiros – Limnetica

Diversity, community structure, and bioremediation potential of mercury-resistant marine bacteria of estuarine and coastal environments of Odisha, India – Hirak R. Dash – Environmental Science and Pollution Research

Review: Microbial Surface Colonization and Biofilm Development in Marine Environments – Hongyue Dang – Microbiology and Molecular Biology Reviews

Bioinformatics and metagenomics

Effect of k-tuple length on sample-comparison with high-throughput sequencing data – Ying Wang – Biochemical and Biophysical Research Communications

Unifying view of stem–loop hairpin RNA as origin of current and ancient parasitic and non-parasitic RNAs, including in giant viruses – Hervé Seligmann – Current Opinion in Microbiology

Alignment behaviors of short peptides provide a roadmap for functional profiling of metagenomic data – Rohita Sinha – BMC Genomics

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis – Phelim Bradley – Nature Communications

Proteomics

Review: The challenge of metaproteomic analysis in human samples – Jonathan M Blackburn – Expert Review of Proteomics

Functional foods

Fermented milk containing Lactobacillus casei strain Shirota prevents the onset of physical symptoms in medical students under academic examination stress – A. Kato-Kataoka – Beneficial Microbes

Microbes in the news

Topical Mupirocin Changes Sinus Microbiome – Interview with Tara F. Carr – Medical Research

Is This Snowy Wonderland Or The World Inside A Petri Dish? – Meredith Rizzo – NPR

End of the year lists

From Blood Rain to Green Poo: 10 Weirdest Science Stories of 2015 – Elizabeth Palermo – Live Science

The Altmetric Top 100 Research Papers 2015 – Altmetric
[hr]

December 23, 2015

Posted on by

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
[hr]