Category Archives: Food Microbiology

December 15, 2015

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Self-tracking the microbiome (quantified self), a human gut-on-a-chip model, indoor air bacteria in residences in the San Francisco Bay Area, and using probiotics on corals during oil spills.

General microbiome

Biometrics’ new identity—measuring more physical and biological traits: Research into the characteristics that are unique to an individual is addressing the need to correctly identify people in a variety of medical, social and security contexts – Andrea Rinaldi – EMBO Reports

Commentary: Self-tracking the microbiome: where do we go from here? – Carine Gimbert – Microbiome

Conference abstracts: 3th ISM World Congress on Targeting Microbiota – Journal of International Society of Microbiota Volume 1 No. 1

Pregnancy and birth

Buccal administration of human colostrum: impact on the oral microbiota of premature infants – K Sohn – Journal of Perinatology

Human mouth/ear microbiome

Pathophysiology of sinusitis of odontogenic origin – Silvio Taschieri – Journal of Investigative and Clinical Dentistry

Human gut microbiome

Different sub-type strains of Akkermansia muciniphila abundantly colonize in southern China – Xianfeng Guo – Journal of Applied Microbiology

Simultaneous fecal microbial and metabolite profiling enables accurate classification of pediatric irritable bowel syndrome – Vijay Shankar – Microbiome

Mucosal Barrier Depletion And Loss Of Bacterial Diversity Are Primary Abnormalities In Paediatric Ulcerative Colitis – Misagh Alipour – Journal of Crohn’s and Colitis

Systematic review with meta-analysis: long-term outcomes of faecal microbiota transplantation for Clostridium difficile infection – Y.-T. Li – Alimentary Pharmacology & Therapeutics

Microbiome models

Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip – Hyun Jung Kim – PNAS

Effects of antibiotics (oxytetracycline, florfenicol or tulathromycin) on neonatal calves’ faecal microbial diversity – J. Oultram – Veterinary Record

Animal microbiome

Metagenomic Assembly Reveals Hosts of Antibiotic Resistance Genes and the Shared Resistome in Pig, Chicken and Human Feces – Liping Ma – Environmental Science & Technology

The impact of rearing environment on the development of gut microbiota in tilapia larvae – Christos Giatsis – Scientific Reports

The characterization and manipulation of the bacterial microbiome of the Rocky Mountain wood tick, Dermacentor andersoni – Katie A. Clayton – Parasites & Vectors

Impact of oil spills on coral reefs can be reduced by bioremediation using probiotic microbiota – Henrique Fragoso ados Santos – Scientific Reports

Plant, root, and soil microbiome

Stronger warming effects on microbial abundances in colder regions – Ji Chen – Scientific Reports

Seasonal dynamics of the microbiome of chernozems of the long-term agrochemical experiment in Kamennaya Steppe – T. I. Chernov – Eurasian Soil Science

Water and extremophile microbiome

Metagenome-assembled genomes uncover a global brackish microbiome – Luisa W. Hugerth – Genome Biology

Similar microbial communities found on two distant seafloor basalts – Esther Singer – Frontiers in Microbiology

Microbial communities on seafloor basalts at Dorado Outcrop reflect level of alteration and highlight global lithic clades – Michael D. Lee – Frontiers in Microbiology

Bacterioplankton dynamics within a large anthropogenically impacted urban estuary – Thomas C. Jeffries – Frontiers in Microbiology

Marine microbial community structure assessed from combined metagenomic analysis and ribosomal amplicon deep-sequencing – Savvas Genitsaris – Marine Biology Research

Groundwater isolation governs chemistry and microbial community structure along hydrologic flowpaths – Sarah Ben Maamar – Frontiers in Microbiology

Review: Forged Under the Sun: Life and Art of Extremophiles from Andean Lakes – Virginia Helena Albarracín – Photochemistry and Photobiology

Food microbiology

Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations – Jinshui Zheng – Scientific Reports

Built environment microbiology

Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences – Marzia Miletto – Microbiome

Review: Antibiotic resistance in urban aquatic environments: can it be controlled? – Célia M. Manaia – Applied Microbiology and Biotechnology

Metagenomics, phages, and bioinformatics

Computational approaches to predict bacteriophage–host relationships – Robert A. Edwards – FEMS Microbiology Reviews

Partial least squares regression can aid in detecting differential abundance of multiple features in sets of metagenomic samples – Ondrej Libiger – Frontiers in Genetics

Techniques

A new fungal large subunit ribosomal RNA primer for high throughput sequencing surveys – Rebecca C Mueller – FEMS Microbiology Ecology

Biofilms

Classic Spotlight: Before They Were Biofilms – George A. O’Toole – Journal of Bacteriology

Microbes in the news

How Bacteria and Brown Fat Can Spur Weight Loss – Mandy Oaklander – Time

A cultural revolution in the study of the gut microbiome – Medical Xpress

Why Your Body Is Like A Rainforest… Micro-Macro Exhibition at Eden features artwork from students at local secondary schools – PirateFM

Italian olive trees are withering from this deadly bacteria – PBS Newshour

Behind the scenes: Microbial biogeography of a university campus – Ashley Ross – MicroBEnet

Irish company makes biggest breakthrough for microbiology testing in dairy industry in 100 years – Independent Ireland

Bacteria, Archaea – Some Methane In Hydraulic Fracturing Is Even More Natural Than Assumed – Science 2.0

Sweet and sticky: Bacteria use sugars to bind to human cells – Phys.org

Science, publishing, and career

The Unwritten Code of Conduct: Each day this week, my supervisor has walked into my office and made verbal demands that I remove content from my beloved blog – The Research Whisperer

A lesson on misleading graphs from the National Review – Lenny Teytelman – The Spectroscope

Women in STEM research: Better Data and Information Sharing Could Improve Oversight of Federal Grant-making and Title IX Compliance – US Government Accountability Office

Why do scientists like anonymity? Lenny Teytelman – Protocols

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December 12, 2015

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Events

3rd Microbiome R&D and Business Collaboration Forum: Europe, 11-12 April, 2016, London

Pregnancy and birth

Study protocol (no data yet): Intestinal microbiota composition after antibiotic treatment in early life: the INCA study – N. B. M. M. Rutten – BMC Pediatrics

Review: The very low birth weight infant microbiome and childhood health – Maureen W. Groer – Birth Defects Research Part C: Embryo Today: Reviews

Review: Development of the infant intestinal microbiome: A bird’s eye view of a complex process – Sharon B. Meropol – – Birth Defects Research Part C: Embryo Today: Reviews

Review: Microbial programming of health and disease starts during fetal life – Petya T. Koleva – Birth Defects Research Part C: Embryo Today: Reviews

Human gut microbiome

Review: Gut microbiota in health and disease: an overview focused on metabolic inflammation – R. Nagpal – Beneficial Microbes

Animal models

Effects of antibiotics (oxytetracycline, florfenicol or tulathromycin) on neonatal calves’ faecal microbial diversity – J. Oultram – Veterinary Record

Water microbiome

Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre – Jessica A Bryant – ISME Journal

Bioprospecting around Arctic islands: Marine bacteria as rich source of biocatalysts
– Concetta De Santi – Journal of Basic Microbiology

Built environment microbiology

Review: Microlayer enrichment in natural treatment systems: linking the surface microlayer to urban water quality – Megan A. Rippy – Wiley Interdisciplinary Reviews: Water

Food microbiology

Dynamics and Diversity of Microbial Community Succession of Surimi During Fermentation with Next-Generation Sequencing – Dandan Zhao – Journal of Food Safety

Infection microbiology

Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics – Brittany Goldberg – mBio

Microbes in the news

Scientist who injected himself with 3.5 million year old bacteria ‘feels fine’ – Brittany A. Roston – Slash Gear

Kim Kardashian Has a Cold: Health issues are the new frontier in celebrity PR – Ruth Graham – Slate

Biotech startup will mine the gut for drugs affecting human behavior – Ike Swetlitz – STAT news

Functions of global ocean microbiome key to understanding environmental changes: Mary Ann Moran – University of Georgia / EurekAlert

Foodstuffs: N.H. Sauerkraut Maker Rides the Microbiome Wave Into Tom Brady’s Pantry (Maybe) – Sam Evans-Brown – NHPR

Kickstarter project: Snotbot, custom-built drones that hover in the air above a surfacing whale and collect the blow (or snot) exhaled from its lungs – Kickstarter
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December 11, 2015

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Mammalian corpse decomposition – beautiful work by Jessica Metcalf.

Microbiome of death

Microbial community assembly and metabolic function during mammalian corpse decomposition – Jessica L. Metcalf – Science

Human oral microbiome

Review: Oral microbiome, periodontitis and risk of head and neck cancer – Leonardo Victor Galvão-Moreira – Oral Oncology

Review: The emerging landscape of salivary diagnostics – Yong Zhang – Periodontology 2000

Review: Influence of saliva on the oral microbiota – Philip D. Marsh – Periodontology 2000

Human skin microbiome

OK, not microbial, but entertaining: A comparative clinical study of different hair removal procedures and their impact on axillary odor reduction in men – Anthony Lanzalaco – Journal of Cosmetic Dermatology

Human respiratory microbiome

Correspondence: Potential roles of disordered airway microbiota in patients with severe asthma – Zongxin Ling – Journal of Allergy and Clinical Immunology

Human gut microbiome

Stress and the Microbiota–Gut–Brain Axis in Visceral Pain: Relevance to Irritable Bowel Syndrome – Rachel D. Moloney – CNS Neuroscience & Therapeutics

Review: SLE: Another Autoimmune Disorder Influenced by Microbes and Diet? – Qinghui Mu – Frontiers in Immunology

Review: The Intestinal Microbiome and the Liver Transplant Recipient: What We Know
and What We Need to Know – Iliana Doycheva

Microbiome models

Vancomycin treatment and butyrate supplementation modulate gut microbe composition and severity of neointimal hyperplasia after arterial injury – Karen J. Ho – Physiological Reports

Can closed artificial ecosystem have an impact on insect microbial community? A case study of yellow mealworm (Tenebrio molitor L.) – Leyuan Li – Ecological Engineering

Plant, root, and soil microbiome

Increasing aridity reduces soil microbial diversity and abundance in global drylands – Fernando T. Maestre – PNAS

The interaction between iron nutrition, plant species and soil type shapes the rhizosphere microbiome – Youry Pii – Plant Physiology and Biochemistry

Nitrification and Nitrifying Bacteria in a Coastal Microbial Mat – Haoxin Fan – Frontiers in Microbiology

Diversity of Phytophthora Species from Declining Mediterranean Maquis Vegetation, including Two New Species, Phytophthora crassamura and P. ornamentata sp. nov. – Bruno Scanu – PLOS ONE

Algae–bacteria interactions: Evolution, ecology and emerging applications – Rishiram Ramanan – Biotechnology Advances

Water microbiome

Particle-Associated Differ from Free-Living Bacteria in Surface Waters of the Baltic Sea – Angelika Rieck – Frontiers in Microbiology

The global ocean microbiome – Mary Ann Moran – Science

Hypothesis: Fractal Hypothesis of the Pelagic Microbial Ecosystem—Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web? – Selina Våge – Frontiers in Microbiology

Food microbiology

Microbiome profiling in fresh-cut products – Chiara Gorni – Trends in Food Science & Technology

FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis – Eugenio Parente – International Journal of Food Microbiology

Bioinformatics and metagenomics

The MG-RAST metagenomics database and portal in 2015 – Andreas Wilke – Nucleic Acids Research

Infection and transplantation

The Interplay of Host Microbiota and Parasitic Protozoans at Mucosal Interfaces: Implications for the Outcomes of Infections and Diseases – Ann-Katrein Bär – PLOS Neglected Tropical Diseases

Viruses and phages

The role of viruses in the evolution of cyanobacteria – S. V. Shestakov – Biology Bulletin Reviews

Microbes in the news

Thousands of unexpected microbes break down our bodies after death – Elizabeth Pennisi – Science
Meet the Necrobiome: The Waves of Microbes That Will Eat Your Corpse – Ed Yong – The Atlantic
Tiny Witnesses: Microbes Can Tell When A Murder Victim Died – Rob Stein – NPR

New Superbug Resistant To All Antibiotics Linked To Imported Meat – Judy Stone – Forbes

Chipotle, E. coli, and more: The surprising truths about food-borne illnesses – Sheila Kaplan – STAT news

What Your Microbiome Wants for Dinner – David R Montgomery and Anne Bikle

Bacteria engineered with synthetic circadian clocks – EurekAlert

Melanoma Meets Microbiome – Kenneth Y. Tsai – NEJM Journal Watch

Can the health of a pregnant woman’s gut influence her baby? – Massey University

Science, publishing, and career

Making the most of the postdoc experience – Lorena Escudero – Frontiers Blog

Should post-publication peer review be anonymous? The PubPeer organisers and two other scholars debate the merits and pitfalls of anonymity in peer review – Times Higher Education

No evidence that gender contributes to personal research funding success in The Netherlands: A reaction to van der Lee and Ellemers – PNAS

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December 8, 2015

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The CF microbiome, microbes attaching to glycoproteins in sweat, gut bacteria make cockroach poop smell attractive for other cockroaches, mycobiome of South African Cabernet vines, and seasonality of Japanese cherry orchard soil fungi.

General microbiome

Perspective: Behavioral Microbiomics: A Multi-Dimensional Approach to Microbial Influence on Behavior – Adam C.-N. Wong – Frontiers in Microbiology

Research highlight: Microbiota-based nutrition plans – Cláudio Nunes-Alves – Nature Reviews Microbiology

Pregnancy and birth

Maternal risk factors for abnormal vaginal flora during pregnancy – Cecilia Tibaldi – International Journal of Gynecology & Obstetrics

Human respiratory microbiome

MiniReview: The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy – Andreia P. Magalhães – Applied Microbiology and Biotechnology

Human oral microbiome

Oral Microbiota and Risk for Esophageal Squamous Cell Carcinoma in a High-Risk Area of China – Xingdong Chen – PLOS ONE

Human skin microbiome

Sweating the small stuff: Glycoproteins in human sweat and their unexplored potential for microbial adhesion – Robyn A Peterson – Glycobiology

Human gut microbiome

Gut microbiota manipulation with prebiotics in patients with non-alcoholic fatty liver disease: a randomized controlled trial protocol – BMC Gastroenterology

Review: Current roles of specific bacteria in the pathogenesis of inflammatory
bowel disease – Lucy McMullen – Microbiology

Animal and bioreactor models

Intestinal microbiota contributes to individual susceptibility to alcoholic liver disease – M Llopis – Gut

Development of a Laboratory Model of a Phototroph-Heterotroph Mixed-Species Biofilm at the Stone/Air Interface – Federica Villa – Frontiers in Microbiology

Animal microbiome

Gut bacteria mediate aggregation in the German cockroach – Ayako Wada-Katsumata – PNAS

The deep-sea glass sponge Lophophysema eversa harbors potential symbionts responsible for the nutrient conversions of carbon, nitrogen and sulfur – Ren-Mao Tian – Environmental Microbiology

Plant, root, and soil microbiome

The Anti-Phytophthora Effect of Selected Potato-Associated Pseudomonas Strains: From the Laboratory to the Field – Anouk Guyer – Frontiers in Microbiology

Defoliation reduces soil biota – and modifies stimulating effects of elevated CO2 – Marie Dam – Ecology and Evolution

Sequence-based Analysis of the Vitis vinifera L. cv Cabernet Sauvignon Grape Must Mycobiome in Three South African Vineyards Employing Distinct Agronomic Systems – Mathabatha E. Setati – Frontiers in Microbiology

Paradox of plant growth promotion potential of rhizobacteria and their actual promotion effect on growth of barley (Hordeum vulgare L.) under salt stress – Massimiliano Cardinale – Microbiological Research

Survey of Annual and Seasonal Fungal Communities in Japanese Prunus mume Orchard Soil by Next-Generation Sequencing – Yoshinao Aoki – Advances in Microbiology

Actinobacterial Diversity in the Sediments of Five Cold Springs on the Qinghai-Tibet Plateau – Jian Yang – Frontiers in Microbiology

Bacterial diversity assessment of pristine mangrove microbial community from dhulibhashani, sundarban using 16S rRNA gene tag sequencing – Pijush Basak – Genomics Data

Microbialites in the shallow-water marine environments of the Holy Cross Mountains (Poland) in the aftermath of the Frasnian–Famennian biotic crisis – Michał Rakociński – Global and Planetary Change

No tillage combined with crop rotation improves soil microbial community composition and metabolic activity – Bingjie Sun – Environmental Science and Pollution Research

Assessing the contribution of fallen autumn leaves to airborne fungi in an urban environment – Peter J. Irga – Urban Ecosystems

Water and extremophile microbiome

Weak Coherence in Abundance Patterns Between Bacterial Classes and Their Constituent OTUs Along a Regulated River – Clara Ruiz-González – Frontiers in Microbiology

Combined Culture-Based and Culture-Independent Approaches Provide Insights into Diversity of Jakobids, an Extremely Plesiomorphic Eukaryotic Lineage – Tomáš Pánek – Frontiers in Microbiology

Metabolic characteristics of dominant microbes and key rare species from an acidic hot spring in Taiwan revealed by metagenomics – Kuei-Han Lin – BMC Genomics

Waste treatment

Microbial community structure associated with the high loading anaerobic codigestion of olive mill and abattoir wastewaters – Hana Gannoun – Bioresource Technology

Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality – Isabel Douterelo – Environmental Biotechnology

Food microbiology

Pyrosequencing reveals bacterial diversity in Korean traditional wheat-based nuruk – Jyotiranjan Bal – Journal of Microbiology

Metagenomics and bioinformatics

Hunting Down Frame Shifts: Ecological Analysis of Diverse Functional Gene Sequences – Michal Strejcek – Frontiers in Microbiology

GenomeTester4: a toolkit for performing basic set operations – union, intersection and complement on k-mer lists – Lauris Kaplinski – GigaScience

Microbes in the news

Cockroaches communicate via bacteria in their feces – Elizabeth Pennisi – Science Magzine

MSU professor trekking to the Amazon to study bacteria of insects that spread disease
– Anne Cantrell, MSU News Service – Bozeman Daily

Bacterial Biofilms: A Charged Environment – Kathryn Calkins – Biomedical Beat

Maintaining Wellness, Starting From Your Gut – Julie Chen – Huffington Post

Fall into Fungi – Alex Alexiev – MicroBEnet

Caps can play a part in cleaning water, not just bottling it – Jim Johnson – Plastic News

Dirty Yamuna water harbours drug-resistant bacteria – Neetu Chandra Sharma – Daily Mail India

Cooperating bacteria isolate cheaters – Phys.org

What you should know about this ‘new’ STD: interview with Raquel Dardik – Kristine Thomason – CNN

Bacteria Hysteria

Bacteria tests: What’s growing beneath your feet? – Alex Osiadacz – KLTV

Science, publication, and career

Five selfish reasons to work reproducibly – Florian Markowetz – Genome Biology

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December 3, 2015

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Microbiomes of gallstones, soil along a bike trip, nematodes in cattle, kiddie pools, and 100 years of phage research.

Pregnancy and birth

Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota – Gabriele Andrea Lugli – Environmental Microbiology

Gut microbiota analysis reveals a marked shift to bifidobacteria by a starter infant formula containing a synbiotic of bovine milk-derived oligosaccharides and Bifidobacterium animalis subsp. lactis CNCM I-3446 – Umberto Simeoni – Environmental Microbiology

Human skin microbiome

Alas no pictures: Microbial colonization of normal skin: direct visualization of 194 skin biopsies – Anika C. Jahns – Anaerobe

Human gut microbiome

Structural robustness of the gut mucosal microbiota is associated with Crohn’s disease remission after surgery – S Mondot – Gut

Metagenomic sequencing of bile from gallstone patients to identify different microbial community patterns and novel biliary bacteria – Hongzhang Shen – Scientific Reports

Improvement in Human Immune Function with Changes in Intestinal Microbiota by Salacia reticulata Extract Ingestion: A Randomized Placebo-Controlled Trial – Yuriko Oda – PLOS ONE

Establishing a Fecal Microbiota Transplant Service for the treatment of Clostridium difficile Infection – Samuel P. Costello – Clinical Infectious Diseases

Review: From Hype to Hope: The Gut Microbiota in Enteric Infectious Disease –
Peter T. McKenney – Cell

Research Highlight: Can Your Microbiome Tell You What to Eat? – Jairam K.P. Vanamala – Cell Metabolism

Review: Nutrition in cancer patients with cachexia: a role for the gut microbiota? – Laure B. Bindels – Clinical Nutrition Experimental

Review: What’s bugging the gut in OCD? A review of the gut microbiome in obsessive-compulsive disorder – Jasmine Turna – Depression and Anxiety

Book Chapter: Bile Acids, the Microbiome and Metabolic Disease-Implications for Surgery – Cyrus Jahansouz – Metabolic Syndrome and Diabetes

Animal and bioreactor models

Gut Microbiota Orchestrates Energy Homeostasis during Cold – Claire Chevalier – Cell

Microbiota-Modulated Metabolites Shape the Intestinal Microenvironment by Regulating NLRP6 Inflammasome Signaling – Maayan Levy – Cell

Levan Enhances Associated Growth of Bacteroides, Escherichia, Streptococcus and Faecalibacterium in Fecal Microbiota – Kaarel Adamberg – PLOS ONE

Animal microbiome

Cattle: Exploring the Gastrointestinal “Nemabiome”: Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities – Russell W. Avramenko – PLOS ONE

Seals: Brain Meta-Transcriptomics from Harbor Seals to Infer the Role of the Microbiome and Virome in a Stranding Event – Stephanie M. Rosales – PLOS ONE

Shrimp: Bacterial concentration and diversity in fresh tropical shrimps (Penaeus notialis) and the surrounding brackish waters and sediment – D. Sylvain Dabadé – International Journal of Food Microbiology

Plant, root, and soil microbiome

Science and art: Soil microbial communities along the route of a venturous cycling trip – Magdalena Nagler – Applied Soil Ecology

Disease suppression in winter wheat from novel symbiosis with forest fungi – Mary Ridout – Fungal Ecology

Multifunctionality and diversity of culturable bacterial communities strictly associated with spores of the plant beneficial symbiont Rhizophagus intraradices – Fabio Battini – Microbiological Research

Plant Host Species and Geographic Distance Affect the Structure of Aboveground Fungal Symbiont Communities, and Environmental Filtering Affects Belowground Communities in a Coastal Dune Ecosystem – Aaron S. David – Plant Microbe Interactions

The impact of charcoal and soil mixtures on decomposition and soil microbial communities in boreal forest – Nathalie Pluchon – Applied Soil Ecology

Endophytic Actinobacteria and the Interaction of Micromonospora and Nitrogen Fixing Plants – Martha E. Trujillo – Frontiers in Microbiology

The microbiome and functions of black soils are altered by dibutyl phthalate contamination – Zhigang Wang – Applied Soil Ecology

Microbiological and faunal soil attributes of coffee cultivation under different management systems in Brazil – D.R. Lammel – Brazilian Journal of Biology

Spatial Patterns in Biofilm Diversity across Hierarchical Levels of River-Floodplain Landscapes – Marc Peipoch – PLOS ONE

Extremophile microbiome

Bacterial biogeography influenced by shelf–basin exchange in the Arctic surface sediment at the Chukchi Borderland – Dukki Han – Environmental Microbiology

Built environment microbiology

First microbiota assessments of children’s paddling pool waters evaluated using 16S rRNA gene-based metagenome analysis – Toko Sawabe – Journal of Infection and Public Health

Summary of Sloan symposium: healthy buildings 2015-Europe – Hal Levin – Microbiome

Waste microbiology

Characterization of a microbial consortium that converts mariculture fish waste to biomethane – Brigit Quinn – Aquaculture

More microbiology

Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus – Carey Lambert – Nature Communications

Phages and viruses

In retrospect: A century of phage lessons – Forest Rohwer & Anca M. Segall – Nature

Science, publishing, and career

Scientific Misconduct: Red Flags: Warning signs that scandal might be brewing in your lab – John R. Thomas Jr – The Scientist

Explaining Retractions: Editors and publishers should use a standardized form to detail why they are pulling papers from the scientific literature – Hervé Maisonneuve and Evelyne Decullier – The Scientist

Self Correction: What to do when you realize your publication is fatally flawed – Kerry Grens – The Scientist

Microbes in the news

Why It’s Time to Map the Microbiome (Kavli Roundtable) – Alan Brown, The Kavli Foundation – LiveScience

Scientists Argue Appendix Might Not Be ‘Irrelevant’ to Our Health, Propose This as the Organ’s Current Function – Liz Klimas – The Blaze

Immune cells make appendix ‘silent hero’ of digestive health – Walter and Eliza Hall Institute – EurekAlert

Bugs Against Disease: Could bacteria help fight colorectal cancer? A collaborative group of Tufts researchers hope to find out – Jacqueline Mitchell – Tufts Now

New research: Intestinal bacteria are affected by antidiabetic drugs – EurekAlert
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December 1, 2015

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African gut microbiota and Entamoeba colonization, cuticular bacteria in social spiders, Arabidopsis leaf and root microbiota, the mineralosphere, bacteria in operating rooms and on a university campus.

Pregnancy and birth

The role of gut microbiota in fetal methylmercury exposure: insights from a pilot study – Sarah E. Rothenberg – Toxicology Letters

Human respiratory microbiome

Corticosteroid therapy and airflow obstruction influence the bronchial microbiome, which is distinct from that of bronchoalveolar lavage in asthmatic airways – Darcy R. Denner – The Journal of Allergy and Clinical Immunology

Human gut microbiome

Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence – Elise R. Morton – PLOS Genetics

Not yet on Nature website: Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota – Forslund K – Nature

Gut microbiome in health and disease: Linking the microbiome-gut-brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases – Shivani Ghaisas – Pharmacology & Therapeutics

Book Chapter: Microbiome in the Critically Ill – Meredith Barrett – Nutrition Support for the Critically Ill

Review: The gut microbiome, diet, and links to cardiometabolic and chronic disorders – Judith Aron-Wisnewsky & Karine Clément – Nature Reviews Nephrology

Microbiome and bioreactor models

A distributed cell division counter reveals growth dynamics in the gut microbiota –
Cameron Myhrvold – Nature Communications

Polymicrobial Oral Infection with Four Periodontal Bacteria Orchestrates a Distinct Inflammatory Response and Atherosclerosis in ApoEnull Mice – Sasanka S. Chukkapalli – PLOS ONE

Aflatoxin B1 induced compositional changes in gut microbial communities of male F344 rats – Jincheng Wang – Toxicological Sciences

PhD thesis: Advanced Computational Tools for Analyzing Microbial Communities for Energy Production Environments – Adam Robbins-Pianka – University of Colorado at Boulder

Escherichia coli Nissle 1917 enhances bioavailability of serotonin in gut tissues through modulation of synthesis and clearance – Jonathan Nzakizwanayo – Scientific Reports

Animal microbiome

Cuticular bacteria appear lethal to social spiders in mixed but not monoculture inoculations – Carl N. Keiser – Current Zoology

Plant, root, and soil microbiome

Not yet on Nature website: Functional overlap of the Arabidopsis leaf and root microbiota – Bai Y – Nature

The Mineralosphere Concept: Mineralogical Control of the Distribution and Function of Mineral-associated Bacterial Communities – Stephane Uroz – Trends in Microbiology

Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia) – Dominik Schneider – Frontiers in Microbiology

The assessment of epiphytic yeast diversity in sugarcane phyllosphere in Thailand by culture-independent method – Rujikan Nasanit – Fungal Biology

Changes in soil physicochemical and microbial properties along elevation gradients in two forest soils – Lei Hu – Scandinavian Journal of Forest Research

Influence of Cadmium and Glucose on Soil Microbial Communities – Aliya Gilmullina – American Journal of Applied Sciences

Convergence of microbial assimilations of soil carbon, nitrogen, phosphorus, and sulfur in terrestrial ecosystems – Xiaofeng Xu – Scientific Reports

Water microbiome

Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages – Magali Lescot – ISME Journal

Impact of a wastewater treatment plant on microbial community composition and function in a hyporheic zone of a eutrophic river – Siavash Atashgahi – Scientific Reports

Built environment microbiology

The first microbial environment of infants born by C-section: the operating room microbes – Hakdong Shin – Microbiome

Microbial biogeography of a university campus – Ashley A. Ross and Josh D. Neufeld – Microbiome

Only on Pubmed as of now: Biofilms in churches built in grottoes – Cennamo P – Science of the Total Environment

Molecular Analysis of Microbial Community Structures in Nigerian Oil Production and Processing Facilities in order to Access Souring Corrosion and Methanogenesis – Chuma Okoro – Corrosion Science

Water heater temperature set point and water use patterns influence Legionella pneumophila and associated microorganisms at the tap – William J. Rhoads – Microbiome

Food microbiology

Selection of aroma compounds for the differentiation of wines obtained by fermenting musts with starter cultures of commercial yeast strains – Florin Vararu – Food Chemistry

Metagenomics and bioinformatics

MetaQUAST: evaluation of metagenome assemblies – Alla Mikheenko – Bioinformatics

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires – Eugen Bauer – Microbiome

Book Chapter: Predicting the Metagenomics Content with Multiple CART Trees – Dante Travisany – Mathematical Models in Biology

Enhanced virome sequencing using targeted sequence capture – Todd N. Wylie – Genome Research

Biofilms and infection

Multi-species biofilms in ecology, medicine, and biotechnology – A. N. Nozhevnikova – Microbiology

Bacterial infection remodels the DNA methylation landscape of human dendritic cells –
Alain Pacis – Genome Research

Survival with a Helping Hand: Campylobacter and Microbiota – Ivana Indikova – Frontiers in Microbiology

Microbes in the news

Microbiome Startup uBiome Will Sequence Poop for the CDC – Sarah Zhang – Wired

Dr. Elizabeth Lindsey, gastroenterologist: FACES of Nashville – Liza Graves – Style

Microbiome Monday: The Bacteria and “The Guinea Pig Doctor” – American Museum of Natural History

The beloved pioneer bread that smells like feet and breaks food safety rules – Natalie Zarrelli – Atlas Obscura

Peer review

Want me to review your manuscript for free? Then be polite… – Ian M Mackay – Virology Down Under
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November 28, 2015

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Events

2nd Microbiome R&D and Business Collaboration Congress – Early registration ends Monday – February/March 2016, Kuala Lumpur, Malaysia

Human oral microbiome

Decreased Diversity of the Oral Microbiota of Patients with Hepatitis B Virus-Induced Chronic Liver Disease: A Pilot Project – Zongxin Ling – Scientific Reports

Human gut microbiome

Altered Fecal Microbiota in Paediatric Inflammatory Bowel Disease – Johanna Maukonen – Journal of Crohn’s and Colitis

Microbiome models

Perspective: Could microbial therapy boost cancer immunotherapy? – Alexandra Snyder – Science

Chronic Zinc Deficiency Alters Chick Gut Microbiota Composition and Function – Spenser Reed – Nutrients

Microbiota is an essential element for mice to initiate a protective immunity against Vaccinia virus – Maurício T. Lima – FEMS Microbiology Ecology

Impacts of Extended Laboratory Rearing on Female Fitness in Florida Colonies of the Parasitoid Spalangia cameroni (Hymenoptera: Pteromalidae) With an Analysis of Wolbachia Strains – E.T. Machtinger – Annals of the Entomological Society of America

Animal microbiome

Fish: Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures – Laetitia G. E. Wilkins – Scientific Reports

Termites: Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites – Karen Rossmassler – Microbiome

Ticks: Emerging horizons for tick-borne pathogens: from the ‘one pathogen–one disease’ vision to the pathobiome paradigm – Muriel Vayssier-Taussat – Future Microbiology

Beetles: Surveying the endomicrobiome and ectomicrobiome of bark beetles: The case of Dendroctonus simplex – Audrey-Anne Durand – Scientific Reports

Coral: Bacterial predation in a marine host-associated microbiome – Rory M Welsh – The ISME Journal

Plant, root, and soil microbiome

Illumina High-Throughput Sequencing and Comparative Analysis of Bacterial Communities in Cherry Orchard Soil – Lingzhi Liu – Toxicological & Environmental Chemistry

Water microbiome

Interannual and cyclone-driven variability in phytoplankton communities of a tropical coastal lagoon – Suchismita Srichandan – Marine Pollution Bulletin

New insights into relationships between active and dormant organisms, phylogenetic diversity and ecosystem productivity – Jacob A. Cram – Molecular Ecology

Metagenomic Analysis of Upwelling-Affected Brazilian Coastal Seawater Reveals Sequence Domains of Type I PKS and Modular NRPS – Rafael R. C. Cuadrat – International Journal of Molecular Sciences

Assessment of bacterial species present in Pasig River and Marikina River soil using 16S rDNA phylogenetic analysis – Maria Constancia O. Carrillo – International Journal of Philippine Science and Technology

Bacterial community composition of an urban river in the North West Province, South Africa, in relation to physico-chemical water quality – K. Jordaan – Environmental Science and Pollution Research

Extremophile microbiome

The impact of temperature on microbial diversity and AOA activity in the Tengchong Geothermal Field, China – Haizhou Li – Scientific Reports

Built environment microbiome

Characterizing the Bacterial Communities in Retail Stores in the United States – A Hoisington – Indoor Air

Viruses and phages

A New Zamilon-like Virophage Partial Genome Assembled from a Bioreactor Metagenome – Meriem Bekliz – Frontiers in Microbiology

Bioinformatics and metagenomics

Bayesian identification of bacterial strains from sequencing data – Aravind Sankar – ArXiv

Microbial Ecology

Resource limitation drives spatial organization in microbial groups – Sara Mitri – The ISME Journal

Genome-scale modelling of microbial metabolism with temporal and spatial resolution – Michael A. Henson – Biochemical Society Transactions

Biofilms / Infection microbiology

Microbial biofilms associated with intravascular catheter-related bloodstream infections in adult intensive care patients – L. Zhang – European Journal of Clinical Microbiology & Infectious Diseases

Review: The limitations of in vitro experimentation in understanding biofilms and chronic infection – Aled E L Roberts – BioRxiv

Review: The Application of Metagenomic Approaches in the Management of Infectious
Diseases – Jinhua Wu – Tropical Medicine & Surgery

Food microbiology

Sourdough microbial community dynamics: An analysis during French organic bread-making processes – Emilie Lhomme – Food Microbiology

Bacteria in the news

Woolly rhino bacteria cleans up oil spills – Energy Global

A personal touch to wine microbiology – Kyanah Lawson – Food Magazine

Arizona inspectors find Theranos lab issues – AZ Central

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November 26, 2015

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Happy Thanksgiving, everyone! NCBI’s Pubmed nor Google Alerts did not take any holiday, so here is a post stuffed (pun intended) with new papers. For today, I got the microbiome of turkey, red wine, and coprolites. And strain-level variation in human-associated bacteria, cat periodontitis, and historical penguin activity too!

General microbiome

Nurturing the microbiome field: It is exciting to see the nucleus of a grand vision for the field, but we must make the fundamentals of the scientific method central to our mission – Pat Schloss – Science

Book: Microbial Endocrinology: Interkingdom Signaling in Infectious Disease and Health
Chapters include:

Pregnancy and birth

Preterm gut microbiota and metabolome following discharge from intensive care – Christopher J. Stewart – Scientific Reports

The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study – Toxicology Letters

Assessing the Intestinal Microbiota in the SHINE Trial – Ethan K. Gough – Clinical Infectious Diseases

Gravidas with Class III Obesity: Evaluating the Abdominal Skin Microbiota Above and Below the Panniculus – Rodney K Edwards – The Journal of Maternal-Fetal & Neonatal Medicine
Review: A Review of Antibiotic Use in Pregnancy – P. Brandon Bookstaver – Pharmacotherapy

Review: On the origin of species: Factors shaping the establishment of infant’s gut microbiota – Niels van Best – Birth Defects Research Part C: Embryo Today: Reviews

Review: Molecular characterization of the human microbiome from a reproductive perspective – Amir Mor – Fertility and Sterility

Review: Reproductive tract microbiome in assisted reproductive technologies – Jason M. Franasiak – Fertility and Sterility

Review: Gynecologic health and disease in relation to the microbiome of the female reproductive tract – Katherine A. Green – Fertility and Sterility

Human skin microbiome

Genetic associations and shared environmental effects on the skin microbiome of Korean twins – Jiyeon Si – BMC Genomics

Human respiratory microbiome

The Sputum Microbiome in Chronic Obstructive Pulmonary Disease Exacerbations
Yvonne J. Huang – Annals of the American Thoracic Society

Review: Clinical Insights into Pulmonary Exacerbations in Cystic Fibrosis from the Microbiome. What Are We Missing? – Fiona J. Whelan – Annals of the American Thoracic Society

Human oral microbiome

Microbiome of titanium and zirconia dental implants abutments – Cássio do Nascimento – Dental Materials

Human gut microbiome

Microbiota and food residues including possible evidence of pre-mammalian hair in Upper Permian coprolites from Russia – Piotr Bajdek – Lethaia

Red wine polyphenols modulate fecal microbiota and reduce markers of the metabolic syndrome in obese patients – Moreno-Indias Isabel – Food & Function

The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism – María V. Selma – Food & Function

The severity of NAFLD is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota – Jérôme Boursier – Hepatology

Differences of microbiota in small bowel and faeces between irritable bowel syndrome patients and healthy subjects – Chen-Shuan Chung – Scandinavian Journal of Gastroenterology

Methodology, Not Concept of Fecal Microbiota Transplantation, Affects Clinical Findings – Bota Cui – Gastroenterology

The Gut-Liver Axis in Primary Sclerosing Cholangitis – Bertus Eksteen – Clinics in Liver Disease

Animal models

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota – Marie Vétizou – Science

Antepartum Antibiotic Treatment Increases Offspring Susceptibility to Experimental Colitis: A Role of the Gut Microbiota – Peris Mumbi Munyaka – PLOS ONE

Metabolomic study on the faecal extracts of atherosclerosis mice and its application in a Traditional Chinese Medicine – Feng Tian – Journal of Chromatography B

Animal microbiome

Temporal Relationships Exist Between Cecum, Ileum, and Litter Bacterial Microbiomes in a Commercial Turkey Flock, and Subtherapeutic Penicillin Treatment Impacts Ileum Bacterial Community Establishment – Jessica L. Danzeisen – Frontiers in Veterinary Science

A Pyrosequencing Investigation of Differences in the Feline Subgingival Microbiota in Health, Gingivitis and Mild Periodontitis – Stephen Harris – PLOS ONE

Phylogenetic and ecological factors impact the gut microbiota of two Neotropical primate species – Katherine R. Amato – Oecologia

Plant, root, and soil microbiome

Bacterial diversity is strongly associated with historical penguin activity in an Antarctic lake sediment profile – Renbin Zhu – Scientific Reports

Elk, sagebrush, and saprotrophs: indirect top-down control on microbial community composition and function – Anna R. Peschel – Ecology

Effect of soil salinity and nutrient levels on the community structure of the root-associated bacteria of the facultative halophyte, Tamarix ramosissima, in southwestern United States – Takeshi Taniguchi – Journal of General and Applied Microbiology

Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots – Bao-Yu Tia – Scientific Reports

Effect of rice straw application on microbial community and activity in paddy soil under different water status – Fuxia Pan – Environmental Science and Pollution Research

Mapping the Centimeter-Scale Spatial Variability of PAHs and Microbial Populations in the Rhizosphere of Two Plants – Amélia Bourceret – PLOS ONE

Diversity of bacterial endophytes in 3 and 15 year-old grapevines of Vitis vinifera cv. Corvina and their potential for plant growth promotion and phytopathogen control – Marco Andreolli – Microbiological Research

Review: Functions, mechanisms and regulation of endophytic and epiphytic microbial communities of plants – Charles W. Bacon – Symbiosis

Review: Culture-independent discovery of natural products from soil metagenomes – Micah Katz – Journal of Industrial Microbiology & Biotechnology

Built environment microbiology

ISS: Extracellular Lipase and Protease Production from a Model Drinking Water Bacterial Community Is Functionally Robust to Absence of Individual Members – Graham G. Willsey – PLOS ONE

Food microbiology

Bacterial Ecology of Fermented Cucumber Rising pH Spoilage as Determined by Nonculture-Based Methods – Eduardo Medina – Journal of Food Science

Microbial Ecology

Complete nitrification by Nitrospira bacteria – Holger Daims – Nature

Does Microbial Diversity Confound General Predictions? – Marie Duhamel – Trends in Plant Science

Metagenomics and bioinformatics

Population genetic analyses of metagenomes reveal extensive strain-level variation in prevalent human-associated bacteria – Stephen Nayfach – BioRxiv

Techniques

Robust and effective methodologies for cryopreservation and DNA extraction from anaerobic gut fungi – Kevin V. Solomon – Anaerobe

Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies – Rashmi Sinha – Cancer Epidemiology, Biomarkers & Prevention

Microbes in the news

Is Double-Dipping Okay? CFUs in 4 types of dips after double dipping – Digg

New Research Reveals Bacteria Associated With Feline Gum Disease for the First Time – PR Newswire

Mission space food: Sugar-growing bacteria go into orbit – Clare Wilson – New Scientist

Your Coffee Machine Is a Breeding Ground for Caffeine-Resistant Bacteria – Matthew Braga – Motherboard

Your Poop Knows Best–New Study Shows Microbiome Can Help Predict Health Responses to Certain Foods – Patrick Mustain – Scientific American

Science, publishing, and career

China pursues fraudsters in science publishing – Mara Hvistendahl – Science
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November 12, 2015

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Gut microbiome and definition of self, symbionts of corals and algae, and microbial geobiology of space exploration. And – yeah! – my Twitter account made it to a “Top 100 Twitter Influencers Working in Life Sciences” list. My Twitter handle is @MicrobiomDigest.

Human gut microbiome

Extensive T-cell epitope repertoire sharing among human proteome, gastrointestinal microbiome, and pathogenic bacteria: implications for the definition of self –
Robert D. Bremel – Frontiers in Immunology

Gut microbiota and diet in patients with different glucose tolerance – Lilit Vanikovna Egshatyan – Endocrine Connections

Review: Alcoholic Liver Disease: The Gut Microbiome and Liver Cross Talk – Phillipp Hartmann – Alcoholism: Clinical and Experimental Research

Review: Linking Microbiota to Human Diseases: A Systems Biology Perspective – Hao Wu – Trends in Endocrinology & Metabolism

Review: Gut microbiota and host metabolism in liver cirrhosis – Makoto Usami – World Journal of Gastroenterology

Infection and cancer microbiology

Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis – Samuel A. Shelburne – PLOS ONE

Animal microbiome

Open Access: Stable and sporadic symbiotic communities of coral and algal holobionts – Eric R. Hester – The ISME Journal

Plant, root, and soil biology

Past water management affected GHG production and microbial community pattern in Italian rice paddy soils – A. Lagomarsino – Soil Biology and Biochemistry

Elemental stoichiometry indicates predominant influence of potassium and phosphorus limitation on arbuscular mycorrhizal symbiosis in acidic soil at high altitude –
Mohammad Haneef Khan – Journal of Plant Physiology

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach – P. Bhattacharyya – Science of The Total Environment

Food microbiology

Monitoring of spoilage and determination of microbial communities based on 16S rRNA gene sequence analysis of whole sea bream stored at various temperatures – Foteini F. Parlapani – LWT – Food Science and Technology

Variation in fungal microbiome (mycobiome) and aflatoxin in stored in-shell peanuts at four different areas of China – Ning Ding – Frontiers in Microbiology

Waste microbiology

Characterization of successional changes in bacterial community composition during bioremediation of used motor oil-contaminated soil in a boreal climate – Lijuan Yan – Science of the Total Environment

Space microbiology

An ESA Roadmap for Geobiology in Space Exploration – Claire R Cousins – Acta Astronautica

Transcriptomics

Protocol: Prokaryotic Metatranscriptomics – Danilo Pérez-Pantoja – Springer Protocols Handbooks

Microbes in the news

Story behind the paper: Porphyrobacter mercurialis, a new species found by #citizenscience and then sent to the #iss – David Coil – MicroBEnet

Getting a flu shot every year? More may not be better – Helen Branswell – STAT news

Dangerous liaison: Bacteria, viruses in league – Bruce Goldman – Stanford Medicine News

Filamentous Bacteriophage Promote Biofilm Assembly and Function – Patrick R. Secor – Cell Host & Microbe

Intestinal Pathogens Change the Microbiome, Cause E. Coli To “Bloom” – Interview with Shannon D. Manning – Medical Research

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November 2, 2015

Posted on by

Overview of key players of the human microbiome in different sites, foals are born with a rich gut microbiome, biogeography of salmon microbiome, bacteria on Chinese glaciers, and the effect of X-rays on the mango microbiome.

General human microbiome

Diversity of key players in the microbial ecosystems of the human body – Ferenc Jordán – Scientific Reports

Pregnancy and birth

Intestinal microbiota in neonates requiring urgent surgery: assessing the role of probiotics using fecal DNA sequencing – Hiroshi Murakami – Pediatric Surgery International

Review: Bacterial munch for infants: potential pediatric therapeutic interventions of probiotics – Mohsin Khurshid – Future Microbiology

Review: Introduction : Microbiome in human reproduction – Jason M. Franasiak – Fertility and Sterility

Correspondence: Vaginal microbiota during pregnancy: Pathways of risk of preterm delivery in the absence of intrauterine infection? – Jeffrey A Keelan – PNAS

Reply to Keelan and Payne: Microbiota-related pathways for preterm birth – Daniel B DiGiulio – PNAS

Human oral microbiome

Microbiomes of Endodontic-Periodontal Lesions before and after Chemomechanical Preparation – Brenda P.F.A. Gomes – Journal of Endodontics

Oral microbiota in patients with atherosclerosis – Frida Fåk – Atherosclerosis

Review: Intermicrobial interactions as a driver for community composition and stratification of oral biofilms – Nicholas S. Jakubovics – Journal of Molecular Biology

Review: The Fungal Biome of the Oral Cavity – Jyotsna Chandra – Candida Species

Human respiratory microbiome

Are bronchoalveolar lavages a good source for microbial profiling? Differences between throat and bronchoalveolar lavage microbiomes – Alexandra Zimmermann – Journal of Medical Microbiology

Human gut microbiome

Donor species richness determines fecal microbiota transplantation success in inflammatory bowel disease – Severine Vermeire – Journal of Crohn’s and Colitis

Gut mucosal microbiome across stages of colorectal carcinogenesis – Geicho Nakatsu – Nature Communications

Review: Gut mycobiota and adenomas – Chunguang Luan – Gut Microbes

Review: Rate of establishing the gut microbiota in infancy has consequences for future health – Shaillay Dogra – Gut Microbes

Animal microbiome

Development of the faecal microbiota in foals – M. C. Costa – Equine Veterinary Journal

Bacterial communities in termite fungus combs are comprised of consistent gut deposits and contributions from the environment – Saria Otani – Microbial Ecology

The biogeography of the atlantic salmon (Salmo salar) gut microbiome – Martin S Llewellyn – The ISME Journal

Exposure to West Nile Virus Increases Bacterial Diversity and Immune Gene Expression in Culex pipiens – Steven D. Zink – Viruses

Plant, root, and soil microbiome

Plant-microbe rhizosphere interactions mediated by Rehmannia glutinosa root exudates under consecutive monoculture – Linkun Wu – Scientific Reports

Drivers of bacterial beta diversity in two temperate forests –  Wang – Ecological Research

Characterizing bacterial assemblages in sediments and aerosols at a dry lake bed in Australia using high-throughput sequencing – Chris Munday – Aerobiologia

Review: Influence of soil microbiota in nurse plant systems – Susana Rodríguez-Echeverría – Functional Ecology

Review: The Role of Plant–Microbe Interactions and Their Exploitation for Phytoremediation of Air Pollutants – Nele Weyens – International Journal of Molecular Sciences

Water and extremophile microbiome

Metagenomic analysis of the bacterial community of the Sea of Azov – D. G. Matishov – Marine Biology

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India – Jhasketan Badhai – Frontiers in Microbiology

High diversity and distinctive community structure of bacteria on glaciers in China revealed by 454 pyrosequencing – Qing Liu – Systematic and Applied Microbiology

Review: Databases of the marine metagenomics – Katsuhiko Mineta – Gene

Waste microbiology

Changes in Microbial Composition of Wastewater During Treatment in a Full-Scale Plant – Marija Kaevska – Current Microbiology

Wastewater treatment and microbial communities in an integrated photo-bioelectrochemical system affected by different wastewater algal inocula – Li Xiao – Algal Research

Review: Microbial diversity in support of anaerobic biomass valorization – M. Jobard – Critical Reviews in Biotechnology

Food microbiology

Effect of X-ray treatments on Escherichia coli O157:H7, Listeria monocytogenes, Shigella flexneri, Salmonella enterica and inherent microbiota on whole mangoes – Barakat S M Mahmoud – Letters in Applied Microbiology

Metagenomics and bioinformatics

Poster: Alignment-free methods for metagenomic profiling – Shanshan Gao – BMC Bioinformatics

Infection microbiology

Microbial diversity on intravascular catheters from paediatric patients – L. Zhang – European Journal of Clinical Microbiology & Infectious Diseases

Phages and viruses

Function of the CRISPR-Cas System of the Human Pathogen Clostridium difficile – Pierre Boudry – mBio

Microbial Ecology

Do modern theories of biodiversity fail to predict commonness and rarity among microbes? – William R. Shoemaker – PeerJ

Strongly Deterministic Population Dynamics in Closed Microbial Communities – Zak Frentz – Physical Review

Microbes in the news

Scientists debate mega-microbiome initiatives: Research standards will advance the field, proponents say, but critics counter that they will stifle creativity – Rachel Becker – Nature

Foals born with rich microbial community in their gut – study – Horsetalk

Halloween: Monster Microbiology, 101: If werewolves and other ghouls existed, they’d surely have microbiomes – Rob Dunn – Science Friday

Bacteria in space – ‘You cannot just open the window’ – Interview with Ralf Möller about microbes found on the ISS – DW

New technique could prevent biofilms on catheters and medical implants – EurekAlert

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