Category Archives: Human gut

May 12, 2016

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Dandruff, archaeological dental calculus methanogens, extreme longevity, UK twins, and dissemination of human-derived bacteria into the Antarctic microbiome.

Pregnancy and birth microbiome

Early-life gut microbiome composition and milk allergy resolution – Supinda Bunyavanich – Journal of Allergy and Clinical Immunology

Human skin microbiome

Dandruff is associated with the conjoined interactions between host and microorganisms – Zhijue Xu – Scientific Reports

Human oral microbiome

Restricted diversity of dental calculus methanogens over five centuries, France – Hong T. T. Huynh – Scientific Reports

Metabolic and Community Synergy of Oral Bacteria in Colorectal Cancer – Kaitlin J. Flynn – mSphere

Peri-implant and periodontal microbiome diversity in aggressive periodontitis patients: a pilot study – Vanessa Sousa – Clinical Oral Implants Research

Human respiratory microbiome

The nasal microbiota in infants with cystic fibrosis in the first year of life: a prospective cohort study – Moana Mika – The Lancet Respiratory Medicine

Examining changes in bacterial abundance in complex communities using next-generation sequencing is enhanced with quantitative PCR – Joshua R. Stokell – Antonie van Leeuwenhoek

Human gut microbiome

Gut Microbiota and Extreme Longevity – Elena Biagi – Current Biology

Enteral feeding reduces metabolic activity of the intestinal microbiome in Crohn’s disease: an observational study – C Walton – European Journal of Clinical Nutrition

Genetic Determinants of the Gut Microbiome in UK Twins – Julia K. Goodrich – Cell Host & Microbe

Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study – Christian Milani – Scientific Reports

Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing – Emily Vogtmann – PLOS ONE

Review: Structural and functional changes within the gut microbiota and susceptibility to Clostridium difficile infection – Caná L. Ross – Anaerobe

Preview: What’s LPS Got to Do with It? A Role for Gut LPS Variants in Driving Autoimmune and Allergic Disease – Taylor Feehley – Cell Host & Microbe

Review: Koch’s postulates, microbial dysbiosis and inflammatory bowel disease – Benjamin P. Willing – Clinical Microbiology and Infection

Review: Impact of gut microbiota on diabetes mellitus – G. Blandino – Diabetes & Metabolism

Review: Microbiota and the nitrogen cycle: Implications in the development and progression of CVD and CKD – David Briskey – Nitric Oxide

Review: Impact of microbial derived secondary bile acids on colonization resistance against Clostridium difficile in the gastrointestinal tract – Jenessa A. Winston – Anaerobe

Review: The microbiome-immune-host defense barrier complex (microimmunosome) and developmental programming of noncommunicable diseases – Rodney R. Dietert – Reproductive Toxicology

Animal experiments

A low dose of an organophosphate insecticide causes dysbiosis and sex-dependent responses in the intestinal microbiota of the Japanese quail (Coturnix japonica) – Eduardo Crisol-Martínez – PeerJ

Structural modulation of gut microbiota by chondroitin sulfate and its oligosaccharide – Qingsen Shang – Macromolecules

Administration of probiotic kefir to mice with Clostridium difficile infection exacerbates disease – Jennifer K. Spinler – Anaerobe

Editorial: Immunology: You Remind Me of a Microbe I Know – Ray Soto and June Round – Current Biology

Forum: Human Microbiota-Associated Mice: A Model with Challenges – Marie-Claire Arrieta – Cell Host & Microbe

Plant, root, and soil microbiome

Geography and agronomical practices drive diversification of the epiphytic mycoflora associated with barley and its malt end product in western Canada – Wen Chen – Agriculture, Ecosystems & Environment
http://www.sciencedirect.com/science/article/pii/S0167880916301669

Revisiting the pink-red pigmented basidiomycete mirror yeast of the phyllosphere –
Alec Cobban – MicrobiologyOpen
http://onlinelibrary.wiley.com/doi/10.1002/mbo3.374/abstract

 

Water and extremophile microbiome

Escherichia coli out in the cold: Dissemination of human-derived bacteria into the Antarctic microbiome – Michelle L. Power – Environmental Pollution

Habitat heterogeneity and connectivity shape microbial communities in South American peatlands – Felix Oloo – Scientific Reports

The Egyptian Red Sea coastal microbiome: A study revealing differential microbial responses to diverse anthropogenic pollutants – Ghada A. Mustafa – Environmental Pollution

Conference Highlight: Decoding Microbial “Relationship Statuses” at OSM 2016 – Kelsey Ellis – Bulletin Limnology and Oceanography

Phages and viruses

Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology – Angela L. Rasmussen – Cell Host & Microbe

Techniques

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface – Pranjul Shah – Nature Communications

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants – Cian J. Hill – Microbiome

Video: Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization – Melis N. Anahtar – JOVE

Microbial Ecology

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments – Scott W. Olesen – PLOS ONE

More microbiology

Self-driven jamming in growing microbial populations – Morgan Delarue – bioRxiv

Review: Advances in Understanding Bacterial Pathogenesis Gained from Whole-Genome Sequencing and Phylogenetics – Elizabeth Klemm – Cell Host & Microbe

Microbes in the news

Osel, Inc.’s Lead Product LACTIN-V Enters Phase 2b Study to Prevent Recurrence of Bacterial Vaginosis– Digital Journal

Bacteria Battle Can Lead to Dandruff – Jennifer Viegas – Discovery
Bacteria the yin and yang of dandruff, says study – MedicalXpress

New Microbiome Research Tool Offers Potential to Revolutionise Drug Development
– PR Newswire

Experts react to ‘waste of money’ headlines against probiotics – Adi Menayang – NutraIngredients

How scientists are harnessing the ice-making powers of bacteria – Zach St. George – The Week

Researchers Engineer Bacteria to Streamline Biofuel Production Process – IndiaWest

New Microbiome Research Tool Offers Potential to Revolutionise Drug Development – PR Newswire

Twin study finds that gut microbiomes run in families – EurekAlert

From the American Urological Association meeting: Gut Bugs Differ in Chronic Prostatitis. Difference in taxa may aid biomarker, researchers say – MedPageToday

In Infants With Necrotizing Enterocolitis, Gut Dysbiosis Precedes Disease – Julie A. Jacob – JAMA

Science, publishing, and career

Reminder to deposit DNA sequences – Mark Blaxter – Science

Unexpected revelations for study volunteer: What health information do researchers owe the volunteers in their studies – Jennifer Couzin-Frankel – Science

Bik’s Picks

WATCH: What happened to astronaut Scott Kelly’s DNA during his year in space – Carl Zimmer – STAT News

May 11, 2016

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Microbiomes in low-income human habitats, graph mining for sequence datasets, and a PhD Comics video on the microbiome.

Events

The Barcelona Debates on The Human Microbiome – June 30th and July 1st, 2016 – Barcelona

2016 Molecular Genetics of Bacteria and Phages Meeting in Madison, Wisconsin – August 8-12

General microbiome

Book: Microbiota of the Human Body – Implications in Health and Disease – Editor: Andreas Schwiertz – Springer

Human skin microbiome

Analysis of Facial Implants for Bacterial Biofilm Formation Using Scanning Electron Microscopy – Thomas J. Walker – JAMA Facial Plastic Surgery

Human gut microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Review: The human gut microbiota and its interactive connections to diet – C. Milani – Journal of Human Nutrition and Dietetics

Editorial: The Bugs Within Our Body: The Human Microbiota – DJ Philpott – Clinical Pharmacology & Therapeutics

Plant, root, and soil microbiome

Fate of classical faecal bacterial markers and ampicillin-resistant bacteria in agricultural soils under Mediterranean climate after urban sludge amendment – Clarissa Gondim-Porto – Science of the Total Environment

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi – Stéphane Hacquard – Nature Communications

Gypsum amendment to rice paddy soil stimulated bacteria involved in sulfur cycling but largely preserved the phylogenetic composition of the total bacterial community – Susanne Wörner – Environmental Microbiology Reports

Built environment microbiome

Interconnected microbiomes and resistomes in low-income human habitats – Erica C. Pehrsson – Nature

Metagenomics and bioinformatics

Graph mining for next generation sequencing: leveraging the assembly graph for biological insights – Julia Warnke-Sommer – BMC Genomics

More microbiology

Phenotypic heterogeneity driven by nutrient limitation promotes growth in fluctuating environments – Frank Schreiber – Nature Microbiology

Microbes in the news

Video: The Hidden World of Microbiomes – PhD Comics

Microbiome Monday: What Are You Made Of? – American Museum of Natural History

How dust from the Sahara fuels poisonous bacteria blooms in the Caribbean – Sarah Kaplan – Washington Post

UGA study finds Saharan dust affects marine bacteria, potential pathogen Vibrio
Vibrio can cause serious illness in humans, other marine organisms – EurekAlert

Thank Me Later: New Planet-Saving Bacteria Eats Switchgrass, Makes Biofuel – Tina Casey – Clean Technica

Game-Changing Bacteria Transmits Tuberculosis Through the Skin – HCP Live

Narrow spectrum antibiotic kills pathogens without killing good bacteria – EurekAlert

Dr Paul Blatchford awarded Emerging Researcher Grant – Press Release: Plant and Food Research

The Eye of a Microbial Camera – Nils Schuergers and Tchern Lenn – Natural History Mag

Science, publishing, and career

There’s a huge gender pay gap for STEM careers — just one year after graduation – Brian Resnick – Vox

Young women in STEM fields earn up to one-third less than men – EurekAlert

Bik’s Non-Microbiology Picks

Coral snakes predict the evolution of mimicry across New World snakes – Alison R. Davis Rabosky – Nature Communications

Meet the scientist debunking every dumb food myth on the internet
For every pseudoscientific blog parroting the latest trend, Yvette d’Entremont has a fact-based response – Diana Duong – Chatelaine

Is it safe to eat a newspaper? A Washington Post columnist is about to find out – Damian Garde – STAT news

May 10, 2016, 2nd edition

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Nitrate and oral microcosms, microbial tryptophan metabolism effects on astrocytes, creating germ free plants, a systematic review of the (lack of) effect of probiotics on the gut microbiome, and a phage/host prediction tool.

Event

Starts today: Food-Microbiome Interaction: Implications for Health & Disease – New York Academy of Sciences and the Quadram Institute at The Royal Society in London

Pregnancy and birth

Prenatal and post-natal exposure to antibiotics and risk of asthma in childhood – J. Metsälä – Clinical & Experimental Allergy

Review: Obesity and overweight: Impact on maternal and milk microbiome and their role for infant health and nutrition – Izaskun Garcia-Mantrana – Molecular Nutrition and Food Research

Human respiratory microbiome

Comparison of two commercial DNA extraction kits for the analysis of nasopharyngeal bacterial communities – Marcos Pérez-Losada – AIMS Microbiology

Human oral microbiome

Nitrate and the Origin of Saliva Influence Composition and Short Chain Fatty Acid Production of Oral Microcosms – Jessica E. Koopman – Microbial Ecology

Human skin microbiome

A systematic review and meta-analysis on Staphylococcus aureus carriage in psoriasis, acne and rosacea – J. E. E. Totté – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups – Deepak Yadav – Gut Pathogens

Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials – Nadja B. Kristensen – Genome Medicine

Tissue Microbiome Profiling Identifies An Enrichment of Specific Enteric Bacteria In Opisthorchis viverrini Associated Cholangiocarcinoma – Kern Rei Chng – EBioMedicine

Editorial: Transkingdom interactions: Liver flukes and the microbiota in cancer – Lisa Osborne – EBioMedicine

Review: Could physical exercise help modulate the gut microbiota in chronic kidney disease? – Marta Esgalhado – Future Microbiology

Review: The Gut Microbiota and Immune System Relationship in Human Graft-versus-Host Disease – Lucrezia Laterza – Mediterranean Journal of Hematology and Infectious Diseases

Review: Gut Immunity and Type 1 Diabetes: a Mélange of Microbes, Diet, and Host Interactions? – David Endesfelder – Current Diabetes Reports

Animal experiments

Rumen and Cecum Microbiomes in Reindeer (Rangifer tarandus tarandus) Are Changed in Response to a Lichen Diet and May Affect Enteric Methane Emissions – Alejandro Salgado-Flores – PLOS ONE

Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants – Sheerli Kruger Ben Shabat – The ISME Journal

Book Chapter: Germ-Free Mice Model for Studying Host–Microbial Interactions – Yogesh Bhattarai – Mouse Models for Drug Discovery – Springer

Animal microbiome

Review: Bioprospecting Sponge-Associated Microbes for Antimicrobial Compounds – Anak Agung Gede Indraningrat – Marine Drugs

Plant, root, and soil microbiome

Wheat seed embryo excision enables the creation of axenic seedlings and Koch’s postulates testing of putative bacterial endophytes – Rebekah J. Robinson – Scientific Reports

Evidence of novel plant-species specific ammonia oxidizing bacterial clades in acidic South African fynbos soils – Jean-Baptiste Ramond – Journal of Basic Microbiology

Plants of the Fynbos biome harbour host species-specific bacterial communities – Tsakani Miyambo – FEMS Microbiology Letters

Extremophile microbiome

In situ hydrogen dynamics in a hot spring microbial mat during a diel cycle – Niels Peter Revsbech – Applied and Environmental Microbiology

Metabolomics

Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor – Veit Rothhammer – Nature Medicine

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands – Bruno Lamas – Nature Medicine

Review: Urolithins, the rescue of ‘old’ metabolites to understand a ‘new’ concept: metabotypes as a nexus between phenolic metabolism, microbiota dysbiosis and host health status – Francisco A. Tomás-Barberán – Molecular Nutrition & Food Research

Metagenomics and bioinformatics –

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data – J. A. Frank – Scientific Reports

OrfM: A fast open reading frame predictor for metagenomic data – Ben J. Woodcroft – Bioinformatics

Phages and viruses

HostPhinder: A Phage Host Prediction Tool – Julia Villarroel – MDPI Viruses

More microbiology

Nonclinical Safety Assessment of SYN-004: An Oral β-lactamase for the Protection of the Gut Microbiome From Disruption by Biliary-Excreted, Intravenously Administered Antibiotics – John F. Kokai-Kun – International Journal of Toxicology

Rapid identification of health care–associated infections with an integrated fluorescence anisotropy system – Ki Soo Park – Science Advances

In situ real-time evaluation of radiation-responsive promoters in the extremely radioresistant microbe Deinococcus radiodurans – Narasimha Anaganti – Journal of Biosciences

Microbes in the news

Stool Bank OpenBiome Is Expanding to Somerville. The bank wants more Boston-area residents to donate – Jamie Ducharme

Do probiotics have an effect on healthy adults? It’s too early to tell – EurekAlert

The Microbiome in Pediatric Rheumatic Diseases – Matthew Stoll – The Rheumatologist

May 10, 2016

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A very selective antibiotic that does not disturb the microbiota, metabolic pathways of the Deepwater Horizon spill, and GI microbiome role in acute myeloid leukemia.

Jobs and events

Postdoc funding opportunity “Microbiology of the built environment”, Alfred P. Sloan Foundation

The 4th Microbiome R&D and Business Collaboration Forum: USA – 3-4 October 2016, La Jolla, San Diego, USA

Human gut microbiome

The role of the gastrointestinal microbiome in infectious complications during induction chemotherapy for acute myeloid leukemia – Jessica R. Galloway-Peña – Cancer

Animal experiments

The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model – Philipp Dirksen – BMC Biology

Editorial: Caenorhabditis microbiota: worm guts get populated – Laura C. Clark – BMC Biology

A Pathogen-Selective Antibiotic Minimizes Disturbance to the Microbiome – Jiangwei Yao – Antimicrobial Agents and Chemotherapy

Waste, pollution, and water treatment microbiology

Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill – Nina Dombrowski – Nature Microbiology

The effects of sodium hypochlorite against selected drinking water-isolated bacteria in planktonic and sessile states – I.B. Gomes – Science of the Total Environment

Microbes in the news

Gut Microbiome Startup CeMeT Aims to Build Reference Database from 10K Volunteers in Germany – Julia Karow – Genome Web

Microbiome linked to infectious complications in AML – Medical Xpress

Narrow-Spectrum Antibiotic Could Spare the Microbiome. A drug that singles out Staphylococcus aureus leaves gut-dwelling microbiota largely intact, a mouse study shows – Amanda B. Keener – The Scientist

Genetic potential of oil-eating bacteria from the BP oil spill decoded – University of Texas at Austin

Fooling the test: Antibiotic-resistant bacteria that look susceptible – Phys.org

A new industry that uses bacteria to remediate old mines? – Jonathan Migneault – Sudbury

The Mighty Microbes of Yellowstone – Scalding water is home to what microbiologists call extremophiles, heat-loving creatures that have figured in many scientific breakthroughs – David Quammen – National Geographic

Science, publishing, and career

John Oliver exposes how the media turns scientific studies into “morning show gossip”
– German Lopez – Vox

Tracking Career Outcomes for Postdoctoral Scholars: A Call to Action – Elizabeth A. Silva – PLOS Biology

With quotes from me: Image manipulation in biomedical papers is commonplace – Maria Burke – Chemistry World

Open-access index delists thousands of journals. Many publications did not reapply after leading directory tightened its quality criteria – Monya Baker

May 7, 2016

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Drosophila male-killing spiroplasma, chitin in potting soil, temperature constraints for complex life, a book on microbial diversity, and monitoring sewer health.

General microbiome

Review: Design, analysis and application of synthetic microbial consortia – Xiaoqiang Jia – Synthetic and Systems Biotechnology

Review: Metabolic network modeling of microbial interactions in natural and engineered environmental systems – Octavio Perez-Garcia – Frontiers in Microbiology

Opinion: Mirror, mirror on the wall: which microbiomes will help heal them all? – Renuka R. Nayak – BMC Medicine

Hypothesis: Do microbiotas warm their hosts? – Eugene Rosenberg – Gut Microbes

Human respiratory microbiome

Microbiome diversity in the sputum of patients with pulmonary tuberculosis – P. Krishna – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Literature review: The gut microbiota: a major player in the toxicity of environmental pollutants? – Sandrine P Claus – NPJ Biofilms and Microbiomes

Impact of Hypocaloric Hyperproteic Diet on Gut Microbiota in Overweight or Obese Patients with Nonalcoholic Fatty Liver Disease: A Pilot Study – Zoltan Pataky – Digestive Diseases and Sciences

n=1: Six-week Diet Correction for Body Weight Reduction and Its Subsequent Changes of Gut Microbiota: A Case Report – Bumjo Oh – Clinical Nutrition Research

Conference abstract: Associations Between Physical Activity and the Intestinal Microbiome of College Freshmen – Corrie M Whisner – The FASEB Journal

Animal experiments

Male-Killing Spiroplasma Alters Behavior of the Dosage Compensation Complex during Drosophila melanogaster Embryogenesis – Becky Cheng – Current Biology

Experimental Evolution on a Wild Mammal Species Results in Modifications of Gut Microbial Communities – Kevin D. Kohl – Frontiers in Microbiology

Conference abstract: Soy positively impacts cecal microbiota of ovariectomized rats selectively bred for low aerobic capacity – Tzu-Wen Liu – the FASEB Journal

Animal microbiome

Midgut Transcriptome of the Cockroach Periplaneta americana and Its Microbiota: Digestion, Detoxification and Oxidative Stress Response – Jianhua Zhang – PLOS ONE

Plants, roots, and soil microbiome

Chitin Mixed in Potting Soil Alters Lettuce Growth, the Survival of Zoonotic Bacteria on the Leaves and Associated Rhizosphere Microbiology – Jane Debode – Frontiers in Microbiology

Litter microbial and soil faunal communities stimulated in the wake of a volcanic eruption in a semiarid woodland in Patagonia, Argentina – Paula Berenstecher – Functional Ecology

Richness and bioactivity of culturable soil fungi from the Fildes Peninsula, Antarctica – Zhuang Ding – Extremophiles

Effect of 35 years inorganic fertilizer and manure amendment on structure of bacterial and archaeal communities in black soil of northeast China – Jianli Ding – Applied Soil Ecology

Conference abstract: Multi-omics of the Soil Microbiome – Janet K Jansson – The FASEB Journal

Review: Life cycle specialization of filamentous pathogens — colonization and reproduction in plant tissues – Janine Haueisen – Current Opinion in Microbiology

Review: Interspecific hybridization impacts host range and pathogenicity of filamentous microbes – Jasper RL Depotter – Current Opinion in Microbiology

Water and extremophile microbiome

From climate models to planetary habitability: temperature constraints for complex life – Laura Silva – arXiv preprint

Macroecological drivers of archaea and bacteria in benthic deep-sea ecosystems – Roberto Danovaro – Science Advances

Snowmelt induced hydrologic perturbations drive dynamic microbiological and geochemical behaviors across a shallow riparian aquifer – Robert Danczak – Frontiers in Earth Science

External controls on the distribution, fabrics and mineralization of modern microbial mats in a coastal hypersaline lagoon, Cayo Coco (Cuba) – Anthony Bouton

Richness and bioactivity of culturable soil fungi from the Fildes Peninsula, Antarctica – Zhuang Ding – Extremophiles

Single-Cell Genome and Group-Specific dsrAB Sequencing Implicate Marine Members of the Class Dehalococcoidia (Phylum Chloroflexi) in Sulfur Cycling – Kenneth Wasmund – mBio

Book: Their World: A Diversity of Microbial Environments – Editors: Christon J. Hurst – Springer

Review: Marine microorganisms as a promising and sustainable source of bioactive molecules – G. Romano – Marine Environmental Research

Waste and pollution microbiology

Hydrogeochemistry and coal-associated bacterial populations from a methanogenic coal bed – Elliott P. Barnharta – International Journal of Coal Geology

Review: Does bioleaching represent a biotechnological strategy for remediation of contaminated sediments? – Viviana Fonti – Science of The Total Environment

Review: Microbial sequencing methods for monitoring of anaerobic treatment of antibiotics to optimize performance and prevent system failure – Sevcan Aydin – Applied Microbiology and Biotechnology

Viruses and phages

Editorial overview: The megaviromes – Didier Raoult – Current Opinion in Microbiology

More microbiology

Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development – Ryan H. Hansen – PLOS ONE

RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria – Kelly C Wrighton – The ISME Journal

Research Highlight: A time to gather chromosomes together – Naomi Attar – Nature Reviews Microbiology

Conference abstract: Metabolic Exchange In Microbial Communities – Andrei Osterman – The FASEB Journal

Microbes in the news

Pipe Dreams: Tapping into the Health Information in Our Sewers – Carrie Arnold – Environmental Health Perspectives

Deep sea microbes may be key to oceans’ climate change feedback – Howard Lee – The Guardian

Exploiting Male Killing Bacteria Could Control Insect Pest Species in the Future – SciCasts

Fifty people warned about possible exposure to drug-resistant bacteria at University of Alberta Hospital – Keith Gerein

May 4, 2016

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Note: If you enjoy this blog, I would very much appreciate a comment here below. Without your support, I might not be able to continue MicrobiomeDigest in its current form and frequency. So please, show your love by leaving a sign of support at the end of this blog. Thank you from the bottom of my heart! – Elies

Culturing the unculturables, a review on social bee microbiotas, the needle mycobiome, and an improved phage search tool.

Jobs and events

Faculty Position – Phage Biology and Microbiome Research, McMaster University, Ontario – Science Careers

Postdoctoral Fellow in Mucosal Immunology and Host-Microbiome Interactions
Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill Cornell Medicine – New York City, United States of America

General microbiome

Review: Microbial contributions to chronic inflammation and metabolic disease – Shanahan, Fergus – Current Opinion in Clinical Nutrition and Metabolic Care

Review: The microbial-mammalian metabolic axis: a critical symbiotic relationship – Chilloux, Julien – Current Opinion in Clinical Nutrition and Metabolic Care

Human gut microbiome

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation – Hilary P. Browne – Nature

(Also oral samples) The role of the gastrointestinal microbiome in infectious complications during induction chemotherapy for acute myeloid leukemia – Jessica R. Galloway-Peña – Cancer

Ecological Effect of Solithromycin on the Normal Human Oropharyngeal and Intestinal Microbiota – Mamun-Ur Rashid – Antimicrobial Agents and Chemotherapy

Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production – David Endesfelder – Microbiome

Clostridium difficile Infection in Patients with Inflammatory Bowel Disease – Nancy Fu – Current Infectious Disease Reports

Review: Interplay between diet, gut microbiota, epigenetic events, and colorectal cancer – Scott J. Bultman – Molecular Nutrition & Food Research

Animal microbiome

Cecal microbiota of Tibetan Chickens from five geographic regions were determined by 16S rRNA sequencing – Xueyan Zhou – Microbiology Open

Variability of Bacterial Communities in the Moth Heliothis virescens Indicates Transient Association with the Host – Heike Staudacher – PLOS ONE

Review: Gut microbial communities of social bees – Waldan K. Kwong and Nancy A. Moran – Nature Reviews Microbiology

Plant, root, and soil microbiome

Mineral Type and Solution Chemistry Affect the Structure and Composition of Actively Growing Bacterial Communities as Revealed by Bromodeoxyuridine Immunocapture and 16S rRNA Pyrosequencing – L. C. Kelly – Microbial Ecology

Habitat conditions and phenological tree traits overrule the influence of tree genotype in the needle mycobiome–Picea glauca system at an arctic treeline ecotone – Pascal Eusemann – New Phytologist

Microbial Metagenomics Reveals Climate-Relevant Subsurface Biogeochemical Processes
Philip E. Long – Trends in Microbiology

Extremophile microbiome

Twenty-Three Species of Hypobarophilic Bacteria Recovered from Diverse Ecosystems Exhibit Growth under Simulated Martian Conditions at 0.7 kPa – Andrew C. Schuerger – Astrobiology

Bioinformatics

Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains – Yemin Lan – Microbiome

Phages and viruses

Inferring phage-bacteria infection networks from time series data – Luis Jover – bioRxiv preprint

PHASTER: a better, faster version of the PHAST phage search tool – David Arndt – Nucleic Acids Research

Techniques

Digital Droplet Multiple Displacement Amplification (ddMDA) for Whole Genome Sequencing of Limited DNA Samples – Minsoung Rhee – PLOS ONE

Microbial Ecology

A conceptual framework for invasion in microbial communities – Marta Kinnunen – The ISME Journal

Microbes in the news

Most Gut Microbes Can Be Cultured. Contrary to the popular thought that many species are “unculturable,” the majority of bacteria known to populate the human gut can be grown in the lab, scientists show – Jyoti Madhusoodanan – The Scientist

Capturing the vast diversity of bacteria in our bodies – Megan Thielking – STAT News

A bitter pill. Josiah Zayner’s gut was making his life hell — so he embarked on an extreme DIY fecal transplant – Arielle Duhaime-Ross – The Verge

Article with video: Your mouth is full of bacteria blooming. And it’s beautiful – Hyacinth Empinado – STAT news

Explore this interactive map of the Gowanus Canal’s slightly scary microbiology – Jason Sayer – Architects Newspaper

The Friendly Viruses, and how they can help with the looming antimicrobial resistance crisis – Peter Speck and Anthony Smithyman – OUP blog

How the Gut Microbiome May be Key in Post-Surgery Organ Failure after Heart Surgery in Children – University of Arizona

Bugs as drugs: Harnessing novel gut bacteria for human health – Medical Xpress

Bacteria carrying bug threatens wine industry – John Bartell – ABC

Autonomous Super Mario-Themed Sewer Robots Live-Stream Neighborhood Microbiome Data – The answer to our health is in our excrement – Nickolaus Hines – Inverse

Bay Area Scientists Join Forces To Help Contain Zika Virus – CBS San Francisco

Breast milk hormones found to impact bacterial development in infants’ guts
Intestinal microbiome of children born to obese mothers significantly different from those born to mothers of healthy weight, CU Anschutz researchers find – EurekAlert

Science, publishing, and career

Dealing with retractions – Paul van der Vet – BioMed Central blog

Propagation of errors in citation networks: a study involving the entire citation network of a widely cited paper published in, and later retracted from, the journal Nature – Paul E. van der Vet and Harm Nijveen – Research Integrity and Peer Review

May 3, 2016

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Counting the microbial species on Earth, goat rumen microbiome development, red kangaroos who died a tragic death, fungi in burgundy vineyards, Archaea in  Yellowstone, and image irregularities at a Pfizer lab in La Jolla.

Jobs and Events

Postdoctoral Fellowship Opportunity: Microbiology of the Built Environment – Sloan Foundation

Bioinformatics for the Microbiome, May 27 – Stanford Center for Genomics and Personalized Medicine, $49

General microbiology

Scaling laws predict global microbial diversity: Earth is home to as many as 1 trillion (10exp12) microbial species – Kenneth J. Locey – PNAS

Pregnancy and birth

Impact of Prematurity and Perinatal Antibiotics on the Developing Intestinal Microbiota: A Functional Inference Study – Silvia Arboleya – MDPI International Journal of Molecular Sciences

Review: Young microbes for adult obesity – M. Serino – Pediatric Obesity

Review: Microbial therapeutic interventions – Nicole G. Grady – Seminars in Fetal and Neonatal Medicine

Human oral microbiome

Microbiome of Deep Dentinal Caries Lesions in Teeth with Symptomatic Irreversible Pulpitis – Isabela N. Rôças – PLOS ONE

Human respiratory tract microbiome

Nasopharyngeal Microbiota, Host Transcriptome and Disease Severity in Children with Respiratory Syncytial Virus Infection – Wouter A.A. de Steenhuijsen Piters – Am J Respir Crit Care Med.

Human reproductive tract microbiome

Detection of DNA viruses in prostate cancer – Vitaly Smelov – Scientific Reports

Human gut microbiome

Effect of probiotic yoghurt on animal-based diet-induced change in gut microbiota: an open, randomised, parallel-group study – T. Odamaki – Beneficial Microbes

Fecal microbiota transplant for Clostridium difficile infection in older adults – William M. Tauxe – Therapeutic Advances in Gastroenterology

Review: Fine-tuning of the mucosal barrier and metabolic systems using the diet-microbial metabolite axis – Motoyoshi Nagai – International Immunopharmacology

Review: Gut Microbiome in CKD: challenges and opportunities – Anitha Nallu – Translational Research

Editorial: Transplanting a Microbial Organ: the Good, the Bad, and the Unknown – Dionysios A. Antonopoulos – mBio

Animal models
A polyphenol-rich fraction obtained from table grapes decreases adiposity, insulin resistance and markers of inflammation and impacts gut microbiota in high-fat-fed mice – Brian Collins – The Journal of Nutritional Biochemistry

Diet-induced obesity, energy metabolism and gut microbiota in C57BL/6J mice fed Western diets based on lean seafood or lean meat mixtures – Jacob Bak Holm – The Journal of Nutritional Biochemistry

Colonic Inflammation Accompanies An Increase of β-Catenin Signaling and Lachnospiraceae/Streptococcaceae in the Hind Gut of High-Fat Diet-Fed Mice – Huawei Zeng – The FASEB Journal

Gut commensal Bacteroides acidifaciens prevents obesity and improves insulin sensitivity in mice – J-Y Yang – Mucosal Immunology

Composition and Predicted Metabolic Capacity of Upper and Lower Airway Microbiota of Healthy Dogs in Relation to the Fecal Microbiota – Aaron C. Ericsson – PLOS ONE

Cultivation and qPCR Detection of Pathogenic and Antibiotic-Resistant Bacterial Establishment in Naive Broiler Houses – J. P. Brooks – Journal of Environmental Quality

Exploring the Goat Rumen Microbiome from Seven Days to Two Years – Lizhi Wang – PLOS ONE

Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection – Juan J. Quereda – PNAS

Animal microbiome

Spatial dynamics of the bacterial community structure in the gastrointestinal tract of red kangaroo (Macropus rufus) – Meirong Li – World Journal of Microbiology and Biotechnology

Assessment of Bacterial Communities in Thirteen Species of Laboratory-Cultured Domestic Mites (Acari: Acaridida) – Jan Hubert – Journal of Economic Entomology

Bacterial community in Haemaphysalis ticks of domesticated animals from the Orang Asli communities in Malaysia – Jing-Jing Khoo – Ticks and Tick-borne Diseases

Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence – Robert A. Quinn – Proceedings of the Royal Society B

Taxonomic and functional diversity of the culturable microbiomes of epigeic earthworms and their prospects in agriculture – Arjun Singh – Journal of Basic Microbiology

Methanogen Diversity in Indigenous and Introduced Ruminant Species on the Tibetan Plateau – Xiao Dan Huang – Archaea

Horse Species Symposium abstracts: Journal of Animal Science
Recent advances in the microbiome and physiology of the hindgut of the horse and dog – F. Camargo
Canine intestinal microbiology and metagenomics: From phylogeny to function – B. C. Guard – Journal of Animal Science
The microbiome of the horse hindgut: History and current knowledge – V. Julliand

Plant, root, and soil microbiome

Bacterial diversity and composition in major fresh produce growing soils affected by physiochemical properties and geographic locations – Jincai Ma – Science of the Total Environment

Microbial diversity limits soil heterotrophic respiration and mitigates the respiration response to moisture increase – Fen-Guo Zhang – Soil Biology and Biochemistry

Total and active microbial communities and phoD as affected by phosphate depletion and pH in soil – Sabine A. Ragot – Plant and Soil

Genetically modified WYMV-resistant wheat exerts little influence on rhizosphere microbial communities – Zhenhua Zhang – Applied Soil Ecology

Loss of testate amoeba functional diversity with increasing frost intensity across a continental gradient reduces microbial activity in peatlands – Vincent E.J. Jassey – European Journal of Protistology

Regional-scale analysis of arbuscular mycorrhizal fungi: the case of burgundy vineyards – Marie-Lara Bouffaud – Oeno One

Review: Role of Plant Growth Promoting Rhizobacteria in Agricultural Sustainability—A Review – Pravin Vejan – MDPI Molecules

Chapter: Mycorrhizas in Agroecosystems – Marcela C. Pagano – Recent Advances on Mycorrhizal Fungi

Water and extremophile microbiome

Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water – Maria Aguilar – The Journal of Eukaryotic Microbiology

Drift in ocean currents impacts intergenerational microbial exposure to temperature – Martina A. Doblin – PNAS

Low Genome Content Diversity of Marine Planktonic Thaumarchaeota – Haiwei Luo – Environmental Microbiology Reports

The distribution, diversity and function of predominant Thermoproteales in high-temperature environments of Yellowstone National Park – Zackary J. Jay – Environmental Microbiology

Multidrug resistance phenotypes are widespread over different bacterial taxonomic groups thriving in surface water – Carlos Narciso-da-Rocha – Science of the Total Environment

A 150-year record of phytoplankton 1 community succession controlled by hydroclimatic variability in a tropical lake – Kweku Afrifa Yamoah – Biogeosciences

Review: Hydrothermal Vents and Methane Seeps: Rethinking the Sphere of Influence – Lisa A. Levin – Frontiers in Marine Science

Review: Microbial associations with macrobiota in coastal ecosystems: patterns and implications for nitrogen cycling – Orissa M Moulton – Frontiers in Ecology and the Environment

Book: Biotechnology of Extremophile – Springer

Waste and pollution microbiology

Revealing colonisation and biofilm formation of an adherent coal seam associated microbial community on a coal surface – Silas H.W. Vick – International Journal of Coal Geology

Enhanced Degradation of Diesel in the Rhizosphere of Lupinus luteus after Inoculation with Diesel-Degrading and Plant Growth-Promoting Bacterial Strains – María Balseiro-Romero – Journal of Environmental Quality

Built environment microbiology

Urban Microbiomes and Urban Agriculture: What Are the Connections and Why Should We Care? – Gary M. King – Sowing Seeds in the City

Bioinformatics, transcriptomics, metagenomics

rnaQUAST: a quality assessment tool for de novo transcriptome assemblies – Elena Bushmanova – Bioinformatics

Feature: Microbiology: the road to strain-level identification – Vivien Marx – Nature Methods

Protocol Book: Data Mining Techniques for the Life Sciences – Springer
Bacterial Genomic Data Analysis in the Next-Generation Sequencing Era – Massimiliano Orsini
Update on Genomic Databases and Resources at the National Center for Biotechnology Information – Tatiana Tatusova
Big Data, Evolution, and Metagenomes: Predicting Disease from Gut Microbiota Codon Usage Profiles – Maja Fabijanić

More microbiology

Riches of phenotype computationally extracted from microbial colonies – Tzu-Yu Liu – PNAS

Microbes in the news

UB’s microbiome hunters. These are exciting times at UB as its work on the human genome and microbiome matures. – Research Foundation for The State University of New York

Video: How Your City Has Its Own Unique Microbiome – Discovery News – YouTube

Wrapping up multiple sclerosis at UCSF – Claire Conway – UC San Francisco

Stalking Cave Bacteria to Make Secret Weapons Against Superbugs: Dr. Naowarat Cheeptham – Sam Grobart – Bloomberg

Seres Therapeutics Announces Achievement of Target Enrollment of SER-109 Phase 2 Study for the Prevention of Recurrent Clostridium difficile Infection – Business Wire

Bacteria use traffic-cop-like mechanism to infect gut. WSU scientists discover mechanism critical to pathogens’ success – EurekAlert

Tesla’s Bioweapon Defense Mode can protect you from bacteria, and reduce pollution
Cars. Tesla’s AC unit is available on the Model X and the new Model S – Alphr

Bacteria Hysteria

This odor-fighting, bacteria-killing underwear is made with pure silver – Christian de Looper – Yahoo Digital Trends
Millions of people are drinking mold and bacteria with their coffee. This is how to avoid it! – David Wolfe

Science, publishing and career

Image integrity concerns in papers from a Pfizer lab – Leonid Schneider – For Better Science

May 2, 2016

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Pregnancy and birth

Review: Impact of early gut microbiota on immune and metabolic development and function – Mei Wang – Seminars in Fetal and Neonatal Medicine

Human oral microbiome

Recent advances in salivary cancer diagnostics enabled by biosensors and bioelectronics –
Saswat Mishra – Biosensors and Bioelectronics

Human gut microbiome

Underlying molecular and cellular mechanisms in childhood irritable bowel syndrome – Bruno P. Chumpitazi – Molecular and Cellular Pediatrics

Plant, root, and soil microbiome

Natural decay process affects the abundance and community structure of Bacteria and Archaea in Picea abies logs – J.M. Rinta-Kanto – FEMS Microbiology Ecology

Built environment microbiome

Ciprofloxacin residue and antibiotic-resistant biofilm bacteria in hospital effluent – Jérôme Ory – Environmental Pollution

Melding the Old with the New: Trends in Methods Used to Identify, Monitor, and Control Microorganisms on Cultural Heritage Materials – Patricia Sanmartín – Microbial Ecology

Pollution and waste microbiology

Effect of thermal pretreatment on the biogas production and microbial communities balance during anaerobic digestion of urban and industrial waste activated sludge – Hajer Ennouri – Bioresource Technology

Food microbiology

Microbiological characterisation and volatiles profile of model, ex-novo, and traditional Italian white wheat sourdoughs – Valery Ripari – Food Chemistry

Microbes in the news

PTSD could be prevented with gut microbes, study suggests – Catharine Paddock – Medical News Today

3 years, 3 countries, 222 children: Big gut data tracks impact of hygiene on microbiome – Will Chu – Nutraingredients

Debunking “microbiome causes autism” myths – Exposing Autism One

DNA Genotek’s microbiome collection and stabilization blog. Advancing microbiome discoveries: An update on our grant winners – Megan McGrath – DNA Genotek

SCSU students present antibiotic research on Capitol Hill – Brian Zahn – New Haven Register

Mumbai: Microbiology students create trim almond truffle – Phorum Dalal – Mid Day

Students get a close up view on microbiology. Presentation demonstrated how bacteria plays a role in everyday life – Carolyn Blackburne – Your 4 State

Enlightening the World of Five-Year-Olds: Hand Washing Activity Shines Light on Germs – University of South Carolina Upstate

Using the microbiome to predict risk of infection following chemotherapy – Emmanuel Montassier & Dan Knights – BioMed Central Blog

Novel, bacteria-repelling biomaterial could increase the success of medical implants – Science Daily

Scientists reveal the secret of antibiotic-resistant bacteria – Phys.org

Citizen-scientists to help swimmers ID bacteria-filled lakes – The Eagle

Science, publishing, and career

This hilarious Twitter account uses Lego to show the realities of academia – Jacinta Bowler – Science Alert

Image Manipulation: Cleaning Up the Scholarly Record – Phil Davis – The Scholarly Kitchen

Bacteria in state’s drinking water is ‘public health crisis’ – Gazette Extra
Bik’s Picks

Five Small Animals That Messed With Big Science – Victoria Jaggard – National Geographic

May 1, 2016

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Events

Bioinformatics for the Microbiome – Stanford Center for Genomics and Personalized Medicine – May 27, 2016

General microbiome

Microbiome sequencing: challenges and opportunities for molecular medicine – Thomas Clavel – Expert Review of Molecular Diagnostics

Human skin microbiome

An In vitro Model for Bacterial Growth on Human Stratum Corneum – Danique A. van der Krieken – Acta Dermato-Venereologica

Human respiratory microbiome

Launching into the Deep: Does the Pulmonary Microbiota Promote Chronic Lung Inflammation and Chronic Obstructive Pulmonary Disease Pathogenesis? – Marc A. Sze – American Journal of Respiratory and Critical Care Medicine

Human gut microbiome

Targeting the gut to protect the bladder: Oral Phage therapy approaches against urinary Escherichia coli infections? – Harald Brüssow – Environmental Microbiology

Characterization of gut microbiota profiles in coronary artery disease patients using data mining analysis of terminal restriction fragment length polymorphism: gut microbiota could be a diagnostic marker of coronary artery disease – Takuo Emoto – Heart and Vessels

Review: Gut microbiota: an Indicator to Gastrointestinal Tract Diseases – Trupti Patel – Journal of Gastrointestinal Cancer

Review: Gut microbiome and kidney disease: a bidirectional relationship – Souhaila Al Khodor – Pediatric Nephrology

Animal models

Akkermansia Muciniphila Protects Against Atherosclerosis by Preventing Metabolic Endotoxemia-Induced Inflammation in Apoe-/- Mice – Jin Li – Circulation

The effects of maternal and post-weaning diet on gut microbiota and glucose metabolism in mice offspring – Jia Zheng – Bioscience Reports

Effect of Dietary Starch Source and Concentration on Equine Fecal Microbiota – Brittany E. Harlow – PLOS ONE

Faecal bacterial composition in dairy cows shedding Mycobacterium avium subsp. paratuberculosis in faeces in comparison with nonshedding cows – Marija Kaevska – Canadian Journal of Microbiology

Molecular exploration of fecal microbiome in quinoa-supplemented obese mice – Jose F. Garcia-Mazcorro – FEMS Microbiology Ecology

Lingonberries alter the gut microbiota and prevent low-grade inflammation in high-fat diet fed mice – Lovisa Heyman-Lindén – Food and Nutrition Research

The influence of fishmeal-free diets on microbial communities in Atlantic salmon Salmo salar recirculation aquaculture systems – Victor Schmidt – Applied and Environmental Microbiology

Insights into the biodiversity of the gut microbiota of broiler chickens – Leonardo Mancabelli – Environmental Microbiology

Maternal exposure to a Western-style diet causes differences in intestinal microbiota composition and gene expression of suckling mouse pups – Wilma T. Steegenga – Molecular Nutrition & Food Research

Animal microbiome

Environmental filtering decreases with fish development for the assembly of gut microbiota – Qingyun Yan- Environmental Microbiology

Global microbialization of coral reefs – Andreas F. Haas – Nature Microbiology

Comparison of Varroa destructor and Worker Honeybee Microbiota Within Hives Indicates Shared Bacteria – Jan Hubert – Microbial Ecology

Review: Diagnosis and interpretation of intestinal dysbiosis in dogs and cats – Jan Suchodolski – The Veterinary Journal

Plant, root, and soil microbiome

Selective isolation of potentially phosphate-mobilizing, biosurfactant-producing and biodegradative bacteria associated with a sub-Arctic, terricolous lichen, Peltigera membranacea – Margrét Auður Sigurbjörnsdóttir – FEMS Microbiology Ecology

Soil Protists in Three Neotropical Rainforests are Hyperdiverse and Dominated by Parasites – Frederic Mahe – bioRxiv

Edaphic properties override the influence of crops on the composition of the soil bacterial community in a semiarid agroecosystem – Luke D. Bainard – Applied Soil Ecology

Effects of land use change on the composition of soil microbial communities in a managed subtropical forest – Xiaoping Guo – Forest Ecology and Management

Bioprospecting of Plant Growth Promoting Bacilli and Related Genera Prevalent in Soils of Pristine Sacred Groves: Biochemical and Molecular Approach – Nathaniel A. Lyngwi – PLOS ONE

Aligning molecular studies of mycorrhizal fungal diversity with ecologically important levels of diversity in ecosystems – Ian R Sanders – The ISME Journal

Dynamics of microbial community composition and soil organic carbon mineralization in soil following addition of pyrogenic and fresh organic matter – Thea Whitman – The ISME Journal

Deterministic assembly processes govern bacterial community structure in the Fynbos, South Africa – I. Moroenyane – Microbial Ecology

Plant nitrogen-use strategy as a driver of rhizosphere archaeal and bacterial ammonia oxidiser abundance – Cécile E. Thion – FEMS Microbiology Ecology

Ecological restoration alters microbial communities in mine tailings profiles – Yang Li – Scientific Reports

Water and extremophile microbiome

Co-occurrence analysis of microbial taxa in the Atlantic Ocean reveals high connectivity in the free-living bacterioplankton – Mathias Milici – Frontiers in Microbiology

Identification of Free-living and Particle-Associated Microbial Communities Present in Hadal regions of the Mariana Trench – Jonathan Tarn – Frontiers in Microbiology

Variation in coastal Antarctic microbial community composition at sub-mesoscale: spatial distance or environmental filtering? – Mario Moreno-Pino – FEMS Microbiology Ecology

Microbial communities and arsenic biogeochemistry at the outflow of an alkaline sulfide-rich hot spring – Zhou Jiang – Scientific Reports

Comparative activity and functional ecology of permafrost soils and lithic niches in a hyper-arid polar desert – J. Goordial – Environmental Microbiology

Built environment microbiome

Melding the Old with the New: Trends in Methods Used to Identify, Monitor, and Control Microorganisms on Cultural Heritage Materials – Patricia Sanmartín – Microbial Ecology

Food microbiology

Overlap of spoilage microbiota between meat and meat processing environment in small-scale vs large-scale retail distribution – Giuseppina Stellato – Applied and Environmental Microbiology

Fermentative capabilities and volatile compounds produced by Kloeckera/Hanseniaspora and Saccharomyces yeast strains in pure and mixed cultures during Agave tequilana juice fermentation – Ivonne Wendolyne González-Robles – Antonie van Leeuwenhoek

Pollution and waste microbiology

The effects of salinity on nitrification using halophilic nitrifiers in a Sequencing Batch Reactor treating hypersaline wastewater – Scientific Reports – You-Wei Cui

Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology of Nitrospira spp.– Alejandro Palomo – The ISME Journal

Bioinformatics and metagenomics

Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2 – Johan Bengtsson-Palme – Ecological Informatics

IPED: a highly efficient denoising tool for Illumina MiSeq Paired-end 16S rRNA gene amplicon sequencing data – Mohamed Mysara – BMC Bioinformatics

Minireview: Tracking strains in the microbiome: insights from metagenomics and models – Ilana L. Brito – Frontiers in Microbiology

Viruses and phages

Review: Endogenized viral sequences in mammals – Nicholas F. Parrish – Current Opinion in Microbiology

Probiotics

Probiotic Cream: Viability of Probiotic Bacteria and Chemical Characterization – Lutfiye Yilmaz-Ersan – Journal of Food Processing and Preservation

Transcriptomics

Use of Metatranscriptomics in Microbiome Research – Stavros Bashiardes – Bioinform Biol Insights

More microbiology

Complex molecular mixtures under cycling gradients as basis for lifes origins – Bert Poolman – bioRxiv

Phylogenomic analysis of lipid biosynthetic genes of Archaea shed light on the ‘lipid divide’ – Laura Villanueva – Environmental Microbiology

Review: Are you my symbiont? Microbial polymorphic toxins and antimicrobial compounds as honest signals of beneficial symbiotic defensive traits – Kai Hillman – Current Opinion in Microbiology

Microbes in the news

Findings from the Gut—New Insights into the Human Microbiome – Karen Weintraub – Scientific American

What our gut tells us about the ‘hygiene hypothesis’ – Veronica Meade-Kelly – MedicalXpress

Russian scientists prove Antarctic bacteria brought from other continents – TASS

Beer made from belly button fluff has a bit of the brewer in every glass – Jenni Ryal – Mashable @7centBrewery

Yep, This Brewery Makes Beer Using Bacteria From People’s Belly Buttons: “7 cent Brewery” – Alec MacDonald – Elite Daily

Bacteria from Burning Tree mastodon survived 13,000 years – Laura Arenschield – Dispatch

Echo Bay woman caught harvesting bacteria at gardening event – Jeff Klassen – Soo Today

Weakened coral reefs are facing the threat of algae colonisation – Kemal Atlay – SBS Australia

Junk Food Is Bad For Plants, Too – How a steady diet of fertilizers has turned crops into couch potatoes – Anne Biklé and David R. Montgomery – Nautilus

From running shoes to carbon sinks: four surprising uses for algae – ABC Future Tense

Science, publishing, and career

“Everyone” Downloads Research Papers Illegally – Science magazine just published a great piece on the utility of Sci-Hub. Unfortunately, its defense of its own business model is flawed – Justin Peters – Slate

April 29, 2016

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After Science’s Microbiome Issue yesterday, today’s digest features Genome Biology’s special Translational Microbiome issue. Papers on detecting colon cancer, Clostridium difficile infection, high-fat diets in mice. Also check out papers on H2 metabolism in the colon, no effects of temperature rise on soil microbiome of wet tropical forests, and ultra-basic springs.

Jobs and events

Nice speaker line-up: May 16-18, Michigan Meeting on Microbial Communities: a deep dive into the world of microbes – University of Michigan

Job opening in our lab: Life Science Research Professional  – Stanford

Pregnancy and birth

Gestational age, mode of birth and breastmilk feeding all influence acute early childhood gastroenteritis: a record-linkage cohort study – Jason P. Bentley – BMC Pediatrics

Human gut microbiome

Special issue Genome Medicine: Translating the microbiome: health and disease, Guest Editor: Curtis Huttenhower

Editorial: A roadmap to translating the microbiome – Rabia Begum – Genome Medicine

Detecting colon cancer using microbiota:  Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions – Nielson T. Baxter – Genome Medicine

Dynamics of the fecal microbiome in patients with recurrent and nonrecurrent Clostridium difficile infection – Anna Maria Seekatz – Genome Medicine

Use of Shotgun Metagenome Sequencing to Detect Fecal Colonization with Multi-Drug Resistant Bacteria in Children – Heidi Andersen – Journal of Clinical Microbiology

Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection – Emmanuel Montassier – Genome Medicine

Impact of Helminth Infection on the Clinical and Microbiological Presentation of Chagas Diseases in Chronically Infected Patients – Fernando Salvador – PLOS Neglected Tropical Diseases

Malaria, helminths and malnutrition: a cross-sectional survey of school children in the South-Tongu district of Ghana – Patrick Ferdinand Ayeh-Kumi – BMC Research Notes

Review: The Microbiome and Mental Health: Looking Back, Moving Forward with Lessons from Allergic Diseases – Alan C. Logan – Clinical Psychopharmacology and Neuroscience

Review: Mechanistic and Technical Challenges in Studying the Human Microbiome and Cancer Epidemiology – Mukesh Verma – Technology in Cancer Research & Treatment

Animal models
Effects of Isoflavone-Enriched Feed on the Rumen Microbiota in Dairy Cows – Jitka Kasparovska – PLOS ONE

Deep-fried oil consumption in rats impairs glycerolipid metabolism, gut histology and microbiota structure – Zhongkai Zhou – Lipids in Health and Disease

Dietary supplementation of Rosmarinus officinalis L. leaves in sheep affects the abundance of rumen methanogens and other microbial populations – Gabriella Cobellis – Journal of Animal Science and Biotechnology

Microorganisms in the rumen and reticulum of buffalo (Bubalus bubalis) fed two different feeding systems – Raul Franzolin – BMC Research Notes

Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet – Douglas Mahana – Genome Medicine

A fish, not the bird: Combined effects of dietary mannan- and fructo-oligosaccharide on growth indices, body composition, intestinal bacterial flora and digestive enzymes activity of regal peacock (Aulonocara stuartgranti) – S. S. Mirzapour-Rezaee – Aquaculture Nutrition

Plant, root, and soil microbiome

The composition, localization and function of low-temperature adapted microbial communities involved in methanogenic degradations of cellulose and chitin from Qinghai-Tibetan Plateau wetland soils – Yumei Dai – Journal of Applied Microbiology

Effect of different levels of nitrogen on rhizosphere bacterial community structure in intensive monoculture of greenhouse lettuce – Jian-Gang Li – Scientific Reports

Pichia kudriavzevii as a representative yeast of North Patagonian winemaking terroir – Silvana M. del Mónaco – International Journal of Food Microbiology

Increases in mean annual temperature do not alter soil bacterial community structure in tropical montane wet forests – Paul C. Selmants – Ecosphere

Water and extremophile microbiome

A role for fungi as parasites in the black box of marine trophic interactions – Thomas A. Richards – Environmental Microbiology Reports

Exploring the metabolic potential of microbial communities in ultra-basic, reducing springs at The Cedars, CA, USA: Experimental evidence of microbial methanogenesis and heterotrophic acetogenesis – Lukas Kohl – Journal of Geophysical Research

Viruses and phages

Minireview: Virus-host interplay in high salt environments – Nina S. Atanasova – Environmental Microbiology Reports

Metagenomics and bioinformatics

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques – Disha Tandon – PLOS ONE

Metabolomics

H2 metabolism is widespread and diverse among human colonic microbes – Patricia G. Wolf – Gut Microbes

Localizing metabolic synthesis in microbial cultures with kinetic mass spectrometry imaging (kMSI) – Katherine Louie – bioRxiv

Viruses and phages

The virome: a missing component of biological interaction networks in health and disease – Scott A. Handley – Genome Medicine

Microbial ecology

Commentary: Bacteriophages or bacteriovores – that is the question: variations on the theme of eating Stenotrophomonas maltophilia – Harald Brüssow – Environmental Microbiology Reports

Microbes in the news

Lots of press coverage for the Science and Genome Medicine special issues today!

Scientists think they’ve found the secret to better poop transplants – Rachel Feltman – The Washington Post

Why Are Your Gut Microbes Different From Mine? To find out, scientists collected poop from thousands of people—but they ended up with more questions than answers – Ed Yong – The Atlantic

Food you eat and medicines you take can alter your gut bacteria in both good and bad ways – Emma Tiller – NH Voice

Special microbiome issue – Science Codex

Gut Microbiome Makeup Influenced by Medication Use, Other Factors – Genome Web

In Dutch: Zijn koffie, rode wijn en chocola nou wel of niet goed voor je? – Sander Voormolen – NRC

Title fail: World’s first microbiome study reveals links between lifestyle and gut flora – EurekAlert

Lifestyle has a strong impact on intestinal bacteria – Medical Xpress

The “Friendly” Bacteria In Your Gut Isn’t As Set At Birth As We Thought – Tom Chivers – BuzzFeed

Gut bacteria may predict risk of life-threatening infections following chemotherapy – Science Daily

What Can Happen When You’re Way Too Clean – Alice Park – Time

10 Bizarre (and Wonderful) Facts About Microbes:truly amazing facts about the human microbiome – Dawn Field – TopTenz

Vancouver couple develops slime-free water dishes for dogs – Eric MacKenzie – Vancouver 24h

Podcast: Microbe Talk, April 2016, Can parasitic worms treat inflammatory diseases?

Some superbugs literally explode when they die, making them even more deadly
Ticking time bomb – Jacinta Bowler – Science Alert

Science, publishing, and career

Unconditional data sharing, plus peer review transparency, is key to research reproducibility – Leonid Schneider – The Winnower

Featuring our paper: Seeing double: Duplicated images plague research papers – Ivan Oransky and Adam Marcus – STAT News

Paper linking fecal transplants to obesity in rats retracted for faked data – Dalmeet Singh Chawla – Retraction Watch