Yearly Archives: 2017

August 10, 2017

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Human urinary microbiome

The microbiome in urogenital schistosomiasis and induced bladder pathologies – Adewale S. Adebayo – PLoS Negl Trop Dis

Human gut microbiome

A 3-dimensional mathematical model of microbial proliferation that generates the characteristic cumulative relative abundance distributions in gut microbiomes – Lena Takayasu – PLoS ONE

Plant, root, and soil microbiome

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence – Yun Kit Yeoh – Nature Communications

Spatiotemporal Variation and Networks in the Mycobiome of the Wheat Canopy – Rumakanta Sapkota – Frontiers in Plant Science

Water and extremophile microbiome

Active microorganisms thrive among extremely diverse communities in cloud water – Pierre Amato – PLoS ONE

Seasonal Analysis of Microbial Communities in Precipitation in the Greater Tokyo Area, Japan – Satoshi Hiraoka – Frontiers in Microbiology

Built environment

The US National Mall Microbiome: A Census of Rhizosphere Bacteria Inhabiting Landscape Turf – Jo Anne Crouch – Crop Science

Microbes in the news

For Healthy Skin, Just Add…Bacteria? – Adam Hurly – GQ

Microbes on the market

Reality vs. hype: A macro look at the microbiome market – Juliet Preston – MedCityNews

Science, publishing, and career

Prof claims victory over ‘#manel’ at microbiome conference – Dan Jackson – Campus Reform

August 9, 2017

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Events and jobs

ASM Journals Fellowship – American Society for Microbiology

General microbiome

A mechanistic Individual-based Model of microbial communities – Pahala Gedara Jayathilake – PLoS ONE

Human vaginal microbiome

Group B Streptococcus and the vaginal microbiota – Geoffrey H Rosen – The Journal of Infectious Diseases

Animal experiments

The microbial metabolite desaminotyrosine protects from influenza through type I interferon – Ashley L. Steed – Science

Development of Inflammatory Bowel Disease is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice – Thomas Sharpton – bioRxiv

Plant, root, and soil microbiome

Microbial Communities as Ecological Indicators of Ecosystem Recovery Following Chemical Pollution – Stéphane Pesce – Microbial Ecotoxicology

Assessment of rhizosphere processes for removing water-borne macrolide antibiotics in constructed wetlands – Yiping Tai – Plant and Soil

Poor-Soil Rhizosphere Enriched with Different Microbial Activities Influence the Availability of Base Elements – Faten Dhaw – Open Journal of Ecology

Water and extremophile microbiome

Impacts of leachates from livestock carcass burial and manure heap sites on groundwater geochemistry and microbial community structure – Man Jae Kwon – PLoS ONE

Built environment

Lignocellulose-Degrading Microbial Communities in Landfill Sites Represent a Repository of Unexplored Biomass-Degrading Diversity – Emma Ransom-Jones – mSphere

Probiotics / prebiotics

Utilization of Pyrosequencing to Monitor the Microbiome Dynamics of Probiotic Treated Poultry (Gallus gallus domesticus) during Downstream Poultry Processing – Vamsy Priya Guttala – Agricultural Sciences

Lactobacillus casei CCFM419 attenuates type 2 diabetes via a gut microbiota dependent mechanism – Gang Wang – Food & Function

Bioinformatics

Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information – Albert Barberán – mSphere

Techniques

Isolation of bacteriophages from air using vacuum filtration technique: An improved and novel method – Bhagyashree Magare – Journal of Applied Microbiology

Microbes in the news

Exploring the Equine Microbiome – Stacey Oke – The Horse

Study: Kitchen sponges carry more bacteria than a toilet – Darren Sweeney – Fox8 Cleveland

August 8, 2017

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Our daily digest for you, with highlights on gut microbiota signatures in Japanese infants with food allergy, salt mash communities affected by the Deepwater Horizon oil spill and a proposed stricter P value for claiming a ‘significant’ result.

Jobs

Microbiology Laboratory Technicians – Australian Clinical Labs

General microbiology

Light controlled 3D micromotors powered by bacteria – Gaszton Vizsnyiczai et al. – Nature Communications

Press: Herding Bacteria Brings Power to 3D-Printed Micromotors – Michael Molitch-Hou – Engineering.com

Review: Zika Virus Protease: An Antiviral Drug Target – Congbao Kang et al. – Trends in Microbiology

Call for papers: Advances in Understanding and Controlling Bacteria-Material Interactions, with a Focus on how Bacteria Sense a Surface – Frontiers

Preprint: Saccharomyces cerevisiae strain YH166: a novel wild yeast for the production of tropical fruit sensory attributes in fermented beverages – Kara Osburn – bioRxiv

Pregnancy and early life

Review: Early-life adversity, epigenetics, and visceral hypersensitivity – S. Liu et al. – Neurogastroenterology & Motility

*Signatures in the gut microbiota of Japanese infants who developed food allergies in early childhood – Masaru Tanaka et al. – FEMS Microbiology Ecology

Animal experiments

Mouse: Dietary perturbations alter the ecological significance of ingested Lactobacillus plantarum in the digestive tract – Xiaochen Yin et al. – Scientific Reports

Abstract: A commensal Bifidobacterium longum strain improves gluten-related immunopathology in mice through expression of a serine protease inhibitor – McCarville JL et al. – Applied Environmental Microbiology

Carrageenan-induced colitis is associated with decreased population of anti-inflammatory bacterium, Akkermansia muciniphila, in the gut microbiota of C57BL/6J mice – Qingsen Shang et al. – Toxicology Letters

Mouse: Estrogen protection against EAE modulates the microbiota and mucosal-associated regulatory cells – Gil Benedek et al. – Journal of Neuroimmunology

Feed-additive probiotics accelerate yet antibiotics delay intestinal microbiota maturation in broiler chicken – Pengfei Gao, Chen Ma and Zheng Sun et al. – Microbiome

Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning – Christopher Staley et al. – Microbiome

Animal microbiome

Supplemental thymol and carvacrol increases ileum Lactobacillus population and reduces effect of necrotic enteritis caused by Clostridium perfringes in chickens – Dafei Yin et al. – Scientific Reports

Plant, root and soil microbiome

Impact of Land-use Change on Vertical Soil Bacterial Communities in Sabah – Hoe Seng Tin et al. – Microbial Ecology

Water and extremophile microbiome

Pilot-scale investigation of sludge reduction in aerobic digestion system with endospore-forming bacteria – Kyu Won Seo et al. – Chemosphere

*Abstract: Salt marsh bacterial communities before and after the Deepwater Horizon oil spill – Engel AS et al. – Salt marsh bacterial communities before and after the Deepwater Horizon oil spill

Phages and viruses

A virulence-associated filamentous bacteriophage of Neisseria meningitidis increases host-cell colonisation – Emmanuelle Bille & Julie Meyer et al. – PLoS Pathogens

Microbes in the news

Cleaning a Dirty Sponge Only Helps Its Worst Bacteria, Study Says – Joanna Klein – NYT

McDonald’s, KFC, Burger King drinks test positive for fecal bacteria – WHDH

Congrats, happy couples: You really do share everything, even skin bacteria – Ellen Scott – Metro

Seasonal bacteria causes odd taste in Sacramento water – KCRA Staff – KCRA3

IIT Delhi team develops a new antibacterial drug-delivery system – R. Prasad – The Hindu

Antibiotics use by India’s poultry farms endangering human lives, says expert – Charu Bahri – Hindustan Times

Can We Encode Medical Records Into Our DNA? – Cathy Cassata – Healthline

Papaya Outbreak Grows to 109 Infected People. But How Does Salmonella Get Inside Produce? – Heather Williams – UnsafeFoods

Microbes on the market

PhoneSoap uses a UV sanitizing system to keep your phone bacteria-free – Ricci Rox – NoteBookCheck

Non-microbiology pick

*The Reproducibility Of Research And The Misinterpretation Of P Values – David Colquhoun – bioRxiv

August 7, 2017

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General microbiome

Viruses in the 21st Century: From the Curiosity-Driven Discovery of Giant Viruses to New Concepts and Definition of Life – Patrick Forterre, Clinical Infectious Diseases

Spatial Organization Plasticity as an Adaptive Driver of Surface Microbial Communities – Arnaud Bridier, Frontiers in Microbiology

Functions and emerging applications of bacteriocins – Michael L Chikindas, Current Opinion in Biotechnology

Pregnancy and early life

Ontogenesis of the Gut Microbiota Composition in Healthy, Full-Term, Vaginally Born and Breast-Fed Infants over the First 3 Years of Life: A Quantitative Bird’s-Eye View – Ravinder Nagpal, Frontiers in Microbiology

Multi-site human microbiome

Profiling of faecal water and urine metabolites among Papua New Guinea highlanders believed to be adapted to low protein intake – Eriko Tomitsuka, Metabolomics

Evidence based selection of probiotic strains to promote astronaut health or alleviate symptoms of illness on long duration spaceflight missions – G.L. Douglas, Beneficial Microbes

Human oral microbiome

Salivary microbiome in non-oral disease: A summary of evidence and commentary – Aneesha Acharya, Archives of Oral Biology

Human gut microbiome

Dysbiotic Proteobacteria expansion: a microbial signature of epithelial dysfunction – Yael Litvak, Current Opinion in Microbiology

Role of gut microbiota in idiopathic nephrotic syndrome in children – Kazunari Kaneko, Medical Hypotheses

A preliminary examination of gut microbiota, sleep, and cognitive flexibility in healthy older adults – Jason R. Anderson, Sleep Medicine

Diarrhea after bariatric procedures: Diagnosis and therapy – Yves M Borbély, World Journal of Gastroenterology

The Intestinal Microbiome and Childhood Obesity – Jessica McCann, Current Pediatrics Reports

Cross-modulation of pathogen-specific pathways enhances malnutrition during enteric co-infection with Giardia lamblia and enteroaggregative Escherichia coli – Luther A. Bartelt, PLoS Pathogens

Animal experiments

Streptococcus pneumoniae colonization is required to alter the nasal microbiota in cigarette smoke-exposed mice – Pamela Shen, Infection and Immunity

Fenugreek galactomannan and citrus pectin improve several parameters associated with glucose metabolism, and modulate gut microbiota in mice  – Miriam G. Shtriker, Nutrition

Animal microbiome

The B Vitamin Nutrition of Insects: The contributions of diet, microbiome and horizontally-acquired genes – Angela E. Douglas, Current Opinion in Insect Science

Effects of Disodium Fumarate on In Vitro Rumen Fermentation, The Production of Lipopolysaccharide and Biogenic Amines, and The Rumen Bacterial Community – Wei Jin, Current Microbiology

Cutaneous Microbial Community Variation across Populations of Eastern Hellbenders (Cryptobranchus alleganiensis alleganiensis) – Obed Hernández-Gómez, Frontiers in Microbiology

Microorganisms associated with microscopic insects Megaphragma amalphitanum and Scydosella musawasensis – A. V. Nedoluzhko, Microbiology

Plant, root, and soil microbiome

Polyphasic characterization of bacteria obtained from upland rice cultivated in Cerrado soil – Lívia Fabiana Braga, Brazilian Journal of Microbiology

Taxonomic and functional patterns across soil microbial communities of global biomes – Melline Fontes Noronha, Science of The Total Environment

Phylloplane bacteria of Jatropha curcas : diversity, metabolic characteristics and growth promoting attributes towards vigor of maize seedling – Garima Dubey, Canadian Journal of Microbiology

Bioorganic fertilizer maintains a more stable soil microbiome than chemical fertilizer for monocropping – Feng Cai, Biology and Fertility of Soils

Root exudates of potato onion are involved in the suppression of clubroot in a Chinese cabbage-potato onion-Chinese cabbage crop rotation – Shaocan Chen, European Journal of Plant Pathology

Isolation, characterization and inter-relationship of Phosphate Solubilizing Bacteria from the Rhizosphere of Sugarcane and Rice – Muhammad Awais, Biocatalysis and Agricultural Biotechnology

Distribution of Rhizosphere and Endosphere Fungi on the First-Class Endangered Plant Cypripedium japonicum – Geun-Hye Gang, Mycobiology

Effects of different nitrogen additions on soil microbial communities in different seasons in a boreal forest – Guoyong Yan, Ecosphere

Temporal assessment of microbial communities in soils of two contrasting mangroves – Janaina Rigonato, Brazilian Journal of Microbiology

Bio-fertilizer application induces soil suppressiveness against Fusarium wilt disease by reshaping the soil microbiome – Wu Xiong, Soil Biology and Biochemistry

Bioorganic fertilizer maintains a more stable soil microbiome than chemical fertilizer for monocropping – Feng Cai, Biology and Fertility of Soils

Comparative metagenomics reveals alterations in the soil bacterial community driven by N-fertilizer and Amino 16® application in lettuce – Apostolos Kalivas, Genomics Data

Genetic Diversity of Nitrogen-Fixing and Plant Growth Promoting PseudomonasSpecies Isolated from Sugarcane Rhizosphere – Hai-Bi Li, Frontiers in Microbiology

A Review of Conventional PCR Assays for the Detection of Selected Phytopathogens of Wheat – Adam Kuzdraliński, Journal of Molecular Microbiology and Biotechnology

Effect of mixed edible bacterial inoculants on the early development of improved cultivars of cocoa (Theobroma cacao L.) in a traditional agroforestry system in northern Oaxaca, Mexico – E. Hipólito-Romero, Argentina Journal of Microbiology

Draft Genome Sequence of Cronobacter sakazakiiGP1999, Sequence Type 145, an Epiphytic Isolate Obtained from the Tomato’s Rhizoplane/Rhizosphere Continuum – Hannah R. Chase, Genome Anouncements

Plant-mediated restriction of Salmonella enterica on tomato and spinach leaves colonized with Pseudomonas plant growth-promoting rhizobacteria – Chiun-Kang Hsu, International Journal of Food Microbiology

Water and extremophile microbiome

Assessment upon heterotrophic microalgae screened from wastewater microbiota for concurrent pollutants removal and biofuel production – Liang Shen, Bioresource Technology

Compositions of the Microbial Consortia Present in Biological Sulphate Reduction Processes During Mine Effluent Treatment – Marja Salo, Mine Water and Circular Economy

An underappreciated hotspot of antibiotic resistance: The groundwater near the municipal solid waste landfill – Qing-Lin Chen, Science of The Total Environment

Methane-Fueled Syntrophy through Extracellular Electron Transfer: Uncovering the Genomic Traits Conserved within Diverse Bacterial Partners of Anaerobic Methanotrophic Archaea – Connor T. Skennerton, mBio

A multi-omics based ecological analysis of coastal marine sediments from Gladstone, in Australia’s Central Queensland, and Heron Island, a nearby fringing platform reef – D.J. Beale, Science of The Total Environment

Glaciers and Ice Sheets As Analog Environments of Potentially Habitable Icy Worlds –  Eva Garcia-Lopez, Frontiers in Microbiology

Changes in microbial community structure in response to changing oxygen stress in column tests of denitrification and selenium reduction – Chiachi Hwang, Mine Water and Circular Economy

Next-generation sequencing for investigating the diversity of microorganisms and pathogenic bacteria in a water source – Yingliang Ge, Tropical Journal of Pharmaceutical Research

Microbial community dynamics in aerated biological fluidized bed (ABFB) with continuously increased p-nitrophenol loads – Fangzhou Ji, Process Biochemistry

Food microbiology

RNA-Based Amplicon Sequencing Reveals Microbiota Development during Ripening of Artisanal versus Industrial Lard d’Arnad – Ilario Ferrocino, Applied and Environmental Microbiology

The individual contribution of starter and non-starter lactic acid bacteria to the volatile organic compound composition of Caciocavallo Palermitano cheese – Valeria Guarrasi, International Journal of Food Microbiology

Antimicrobial resistance of Lactobacillus spp. from fermented foods and human gut – Qinqin Ma, LWT – Food Science and Technology

Probiotics / prebiotics

Applications of prebiotics in food industry: A review – Vinti Singla,
Food Science and Technology International

Human milk oligosaccharide consumption by probiotic and human-associated bifidobacteria and lactobacilli – Taksawan Thongaram, Journal of Dairy Science

Probiotic properties of Weissella cibaria and Leuconostoc citreum isolated from tejuino – A typical Mexican beverage – Monique Suela Silva, LWT – Food Science and Technology

A Consumer’s Guide for Probiotics: 10 Golden Rules for a Correct Use – Marco Toscano, Digestive and Liver Disease

Bioinformatics

PATRIC as a unique resource for studying antimicrobial resistance – Dionysios A. Antonopoulos, Briefings in Bioinformatics

Techniques

Optimized experimental workflow for tandem mass spectrometry molecular networking in metabolomics – Florent Olivon, Analytical and Bioanalytical Chemistry

Microbes in the news

Taking too many antibiotics to treat eczema may worsen your condition – DR. LESLIE BAUMANN, Miami Herald

August 5, 2017

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General microbiome

Stay connected: Electrical conductivity of microbial aggregates – C Li – Biotechnology Advances

Preprint: Anti-infective potential of a quorum modulatory polyherbal extract (Panchvalkal) against certain pathogenic bacteria – P Patel – bioRxiv

 

Human respiratory microbiome

Fungal and Bacterial Diversity of Airway Microbiota in Adults with Cystic Fibrosis: Concordance Between Conventional Methods and Ultra-Deep Sequencing, and Their Practical use in the Clinical Laboratory. – F Botterel – Mycopathologia

 

Human skin microbiome

The skin microbiome and immune system: Potential target for chemoprevention? – MA Sherwani – Photodermatol. Photoimmunol. Photomed.

 

Human gut microbiome

Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children – HC The – Gut Microbes

Heritable components of the human fecal microbiome are associated with visceral fat – CI Le Roy – Gut Microbes

Gut-Liver Axis Derangement in Non-Alcoholic Fatty Liver Disease – M Poeta – Children (Basel)

Review:Antigen-specific regulatory T-cell responses to intestinal microbiota – EV Russler-Germain – Mucosal Immunol.

Review:Sulfur Cycling and the Intestinal Microbiome – LL Barton – Dig. Dis. Sci.

Mucosal microbiome dysbiosis in gastric carcinogenesis – OO Coker – Gut

 

Animal microbiome 

Recent developments in understanding the role of the gut microbiota in brain health and disease – E Sherwin – Ann. N. York Acad. Sc

Review:The Gut Microbiome and Mental Health: Implications for Anxiety- and Trauma-Related Disorders – S Malan-Muller – Omics

Phylogenetic diversity and functional characterization of the Manila clam microbiota: a culture-based approach. – L Leite – Environ Sci Pollut Res Int.

 

Plant, root, and soil microbiome

Environment and geographic distance differ in relative importance for determining fungal community of rhizosphere and bulk soil – Kaoping Zhang – Environmental Microbiology

Below- and above-ground effects of deadwood and termites in plantation forests – MD Ulyshen – Ecosphere

Effects of biosolids from a wastewater treatment plant receiving manufactured nanomaterials on Medicago truncatula and associated soil microbial communities at low nanomaterial concentrations – C Chen – Sci Total Environ.

Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils – MC Alvarez-Silva – PLoS One

The Aboveground Vegetation Type and Underground Soil Property Mediate the Divergence of Soil Microbiomes and the Biological Interactions – SH Wu – Microbial Ecology

 

Water microbiome and extremophiles

Preprint: A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer – B Tully – bioRxiv

 

Built environment 

Salt-tolerance aerobic granular sludge: formation and microbial community characteristics – O Doung – Bioresource Technology

Airborne bacterial assemblage in a zero carbon building: a case study – MHY Leung – Indoor Air

 

Microbes in space

Anaerobic microorganisms in astrobiological analogue environments: from field site to culture collection – CS Cockell – International Journal of Astrobiology

 

 

Phages and viruses

Bacteriophages as potential new mammalian pathogens. – GV Tetz – Scientific Reports

 

Techniques

Preprint: An Efficient Moments-Based Inference Method for Within-Host Bacterial Infection Dynamics – D Price – bioRxiv

Novel co-culture plate enables growth dynamic-based assessment of contact-independent microbial interactions – Jr TJ Moutinho – PloS One

PCR cycles above routine numbers do not compromise high-throughput DNA barcoding results – J. Vierna – Genome

Assessment of Bacteria and Archaea in Metalworking Fluids Using Massive Parallel 16S rRNA Gene Tag Sequencing – N. Di Maiuta – Letters in Applied Microbiology

Exploring the microbiome of healthy and diseased peri-implant sites using Illumina Sequencing – I Sanz-Martin – J. Clin. Periodontol.

Isolation and Laboratory Domestication of Natural Yeast Strains – G Liti – Cold Spring Harb Protoc.

 

Microbes in the news

How Metagenomics Are Advancing Infectious Disease Diagnostics – Medscape

Human Microbiome Market Trend to 2022 Profiling Merck, DuPont, MicroBiome Therapeutics, Osel, Vedanta BioSciences & More – MedGadget

New Mexico Tech scientist finds cure for plant disease – El Defensor Chieftain

Permitting pain – Nature Reviews Neuroscience

When He’s Not Charting a Course for the Moon, This Entrepreneur Is Planning Big Things for Your Gut – Inc.

What you eat will protect you from flu — but only if you have the right gut bacteria – Coach

How a tick gut gene serves as a gateway for Lyme disease – YaleNews

Methane-Eating Bacteria Discovered Under The Antarctic Shelf – Iflscience

Blueberries and black tea can help your gut bacteria fight the flu – Cosmos

Microbiology Professor Wanted for Murder – The Scientist

Judge halts Margate sand dune project due to bacteria-filled ponds – NJ

August 3, 2017

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The impact of root hairs on rhizosphere soil structure, gut virome dynamics in hematopoietic stem cell transplantation, an art installation made from bacteria found in a 300-year-old copy of Ovid’s Metamorphoses.

Events and jobs

Assistant/Associate Professor of Soil Microbiomes – Colorado State University

Research Lab Tech Intermediate – University of Michigan Center for Microbial Systems Molecular Biology Laboratory

Content, Lead bioRxiv – Cold Spring Harbor Laboratory

General microbiome

Perspective: The evolution of the host microbiome as an ecosystem on a leash – Kevin R Foster – Nature

Animal experiments

Gut Microbiota Modifies Olfactory-Guided Microbial Preferences and Foraging Decisions in Drosophila – Adam Chun-Nin Wong – Current Biology

Cxcr2 signaling and the microbiome suppress inflammation, bile duct injury, and the phenotype of experimental biliary atresia – Junbae Jee – PLOS ONE

Commensal microbiota-induced microRNA modulates intestinal epithelial permeability through a small GTPase ARF4 – Kazuaki Nakata – Journal of Biological Chemistry

Early life antibiotic exposure causes intestinal dysbiosis and exacerbates skin and lung pathology in experimental systemic sclerosis – Heena Mehta – Journal of Investigative Dermatology

16S rRNA genes Illumina sequencing revealed differential cecal microbiome in specific pathogen free chickens infected with different subgroup of avian leukosis viruses – Xinxin Ma – Veterinary Microbiology

Plant, root, and soil microbiome

High-resolution synchrotron imaging shows that root hairs influence rhizosphere soil structure formation – Nicolai Koebernick – New Phytologist

Genome-Wide Sensitivity Analysis of the Microsymbiont Sinorhizobium meliloti to Symbiotically Important, Defensin-Like Host Peptides – Markus F F Arnold – mBio

Water and extremophile microbiome

Preprint: Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico “Dead Zone” – J Cameron Thrash – bioRxiv

Food microbiology

Fate of Listeria innocua during production and ripening of smeared hard cheese made from raw milk – P Hammer – Journal of Dairy Science

Probiotics/prebiotics

Review: Systematic review: probiotics for functional constipation in children – Katarzyna Wojtyniak – European Journal of Pediatrics

Phages and viruses

The eukaryotic gut virome in hematopoietic stem cell transplantation: new clues in enteric graft-versus-host disease – Jérôme Legoff – Nature Medicine

Metabolomics

The Opportunities of Metabolomics in Drug Safety Evaluation – Pengcheng Wang – Current Pharmacology Reports

More microbes

SnapShot: Electrochemical Communication in Biofilms – Dong-yeon D Lee – Cell

Microbes in the news

Microbiome: Does it really matter to our health? – Jo Seed – Imperial College London

Lovers Share Colonies of Skin Microbes, Study Finds – Aneri Pattani – New York Times

Scientists map the distribution of antimicrobial resistance across Chinese major cities – EurekAlert

Bacteria could be key to freeing South Pacific of mosquitoes – Emma Maris – Nature

Microbiology: The case of the mysterious messenger – Kaitlin Johnson – Nature

Microbes on the market

World’s First DNA and Microbiome Platform Enters the UK Market – Business Wire

IDbyDNA and ARUP Laboratories Announce Partnership to Develop and Commercialize Novel Infectious Disease Testing Using Metagenomics – PR Newswire

Bacteria art

Bacteria from 300-year-old Ovid poetry volume inspires ‘bio-artist’ – Maev Kennedy – The Guardian

Science, career, and publishing

Preprint: The reproducibility of research and the misinterpretation of P values – David Colquhoun – bioRxiv

Preprint: The GSS is an unreliable indicator of biological sciences postdoc population trends – Christopher L Pickett – bioRxiv

The Plan to End Science’s Sexist #manel Problem – Sarah Scoles – WIRED

  • Featuring Elisabeth Bik!

Non-microbiology picks

Proteins evolve on the edge of supramolecular self-assembly – Hector Garcia-Seisdedos – Nature

August 2, 2017

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Enjoy your new  Microbiome Digest with some hot news on this very hot day. Methane- eating microbes found in lake deep beneath Antarctic ice sheet, while some some unexpected life was also found at the bottom of high Arctic Lakes.

 

Human respiratory microbiome
Distal airway microbiome is associated with immunoregulatory myeloid cell responses in lung transplant recipients – Nirmal S. Sharma – The Journal of Heart and Lung Transplatation
Human oral microbiome

 
The oral microbiota in patients with pancreatic cancer, patients with IPMNs, and controls: a pilot study – Sara H. Olson – Cancer Causes & Control

 
Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules – Anna Edlund –  mSystems
Prevalence of periodontal pathogens among italian patients with chronic periodontitis: a retrospective study on 2992 patients – L. Tettamanti- Oral & Implantology

 

 

Human gut microbiome

 
Metabolites and microbial composition of stool of women with fecal incontinence: Study design and methods – Lily A. Arya – Neurology Urodynamics

 
Microscopic Colitis After Fecal Microbiota Transplant – Matthew J. Fasullo – ACG Case Reports Journal
Alteration in the gastric microbiota and its restoration by probiotics in patients with functional dyspepsia – Muneki Igarashi  – BMJ Open Gastroenterology

 
Aggravation of collagen-induced arthritis by orally administered Porphyromonas gingivalis through modulation of the gut microbiota and gut immune system – Keisuke Sato – Scientific Reports

 
The gut microbiota, a new cardiovascular risk factor? – Caroline Chong-Nguyen – La Presse Médicale

 
The Association between Cardiorespiratory Fitness and Gut Microbiota Composition in Premenopausal Women – Yifan Yang – Nutrients

 
Gut microbiota metabolites for sweetening type I diabetes – Thamer Aljtaily – Cellular & Molecular Immunology

 
Vasopressin deletion is associated with sex-specific shifts in the gut microbiome – Christopher T. Fields – Gut Microbes

 
Stable engraftment of human microbiota into mice with a single oral gavage following antibiotic conditioning –  Christopher Staley – Microbiome

 
Animal microbiome 

 
Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling – Renee M. Petri – PLOS One

 
Plant, root, and soil microbiome

 
Activity, biomass and composition of microbial communities and their degradation pathways in exposed propazine soil – C. Jiang  – Ecotoxicology and Environmental Safety

 
Response of microbial community and catabolic genes to simulated petroleum hydrocarbon spills in soils/sediments from different geographic locations– Qinglong Liu – Journal of Applied Microbiology

 
Primary productivity as a control over soil microbial diversity along environmental gradients in a polar desert ecosystem – Kevin M. Geyer – PeerJ

 
Steering Soil Microbiomes to Suppress Aboveground Insect Pests – Ana Pineda –  Trends in Plant Science

 
Importance of exposure dynamics of metal-based nano-ZnO, -Cu and -Pb governing the metabolic potential of soil bacterial communities  – Yujia Zhai – Ecotoxicology and Environmental Safety

 
Water and extremophile microbiome 

 
Production and degradation of fluorescent dissolved organic matter derived from bacteria –  Ken Arai – Journal of Oceanography

 
Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition – Adriana Alberti – Scientific Data
Watershed Urbanization Linked to Differences in Stream Bacterial Community Composition – Jacob D. Hosen – Frontiers in Microbiology

 
Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank – Jessica M. Labonté – Frontiers in Microbiology

 
Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera – Samuel T. Wilson – Nature Microbiology

 
The global biogeography of amino acid variants within a single SAR11 population is governed by natural selection – Tom O. Delmont – bioRxiv

 

Food microbiology

 
Microorganisms in Fermented Apple Beverages: Current Knowledge and Future Directions – Fabien J. Cousin – Microorganisms

 
Probiotics / prebiotics

 
Next-generation probiotics targeting Clostridium difficile through precursor-directed antimicrobial biosynthesis – Jennifer K. Spinler – Infection and Immunity

 
Biotechnology
Forum: Genetically Engineered Bacteria for Treating Human Disease – Buyun Ma – Trends in Pharmacological Sciences

 

Microbes in news

 

Methane-eating microbes found beneath Antarctica’s melting ice sheets

Unexpected Life Found at the Bottom of High Arctic Lakes

Tracking microbial succession in petroleum wells

August 1, 2017

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Today’s digest is relatively short, but there is an amazing commentary on rhizosheath and advantages of using phylogenetic distances to examine the microbial communities

Human gut microbiome

Maternal modifiers of the infant gut microbiota: metabolic consequences

Mulligan CM. Journal of Endocrinology

Association between gut microbiota and bone health: potential mechanisms and prospective

Chen YC. The Journal of Clinical Endocrinology & Metabolism

Plant, soil, and air microbiome

Amynthas agrestis invasion increases microbial biomass in Mid-Atlantic deciduous forests

Chang CH. Soil Biology and Biochemistry

Effect of nanoparticles on crops and soil microbial communities

Rajput VD. Journal of Soils and Sediments

Bottom-up effects on herbivore-induced plant defences: a case study based on compositional patterns of rhizosphere microbial communities.

Benítez E. Scientific reports

Unwrapping the rhizosheath

Pang J. Plant and Soil

Marine and inland waters

Marine archaea and archaeal viruses under global change

Danovaro R-F1000 Research

Bacterial community structure in the intertidal biofilm along the Yangtze Estuary, China

Guo X .Marine Pollution Bulletin

Fronts at the surface ocean can shape distinct regions of microbial activity and community assemblages down to the bathypelagic zone: The Azores Front as a case study

Baltar F. Frontiers in Marine Science

Microbiome Approaches/Techniques

A deep metaproteomics approach for the study of human microbiomes

Zhang X Analytical Chemistry, 2017

Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities.

Shankar V. Scientific reports

Oral/Nasal Microbiome 

The periodontal war: microbes and immunity

Ebersole JL. PERIODONTOLOGY 2000

Design and validation of a DNA-microarray for phylogenetic analysis of bacterial communities in different oral samples and dental implants

Parolin C. Scientific Reports

Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case–control study

Mika M. Microbiome

Food Microbiology 

Comparison study of the volatile profiles and microbial communities of Wuyi Qu and Gutian Qu, two major types of traditional fermentation starters of Hong Qu glutinous rice wine

Liu Z.Food Microbiology

Plant-mediated restriction of Salmonella enterica on tomato and spinach leaves colonized with Pseudomonas plant growth-promoting rhizobacteria

Hsu CK.International Journal of Food Microbiology, 2017

July 31, 2017

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Short digest today, with many articles from Applied and Environmental Microbiology (AEM)!

General microbiome
Review: Bacterial infection increases risk of carcinogenesis by targeting mitochondria – Jesper A.B. Strickertsson – Seminars in Cancer Biology

Pregnancy and early life
Iron in Micronutrient Powder Promotes an Unfavorable Gut Microbiota in Kenyan Infants – Minghua Tang – Nutrients

Multi-site human microbiome
Review: Role of uremic toxin indoxyl sulfate in the progression of cardiovascular disease – Huichang Gao – Life Sciences

Human gut microbiome
The sortase-dependent fimbriome of the genus Bifidobacterium: extracellular structures with potential to modulate microbe-host dialogue – Christian Milani – Applied and Environmental Microbiology

Repression of Salmonella host cell invasion by aromatic small molecules from the human fecal metabolome – Rafael J.M. Peixoto – Applied and Environmental Microbiology

Animal experiments
Antibiotic-Induced Microbiota Dysbiosis Impairs Neuromuscular Function in Juvenile Mice – Valentina Caputi – British Journal of Pharmacology

10-oxo-12(Z)-octadecenoic acid, a linoleic acid metabolite produced by gut lactic acid bacteria, enhances energy metabolism by activation of TRPV1 – Minji Kim – FASEB

Water and extremophile microbiome
Dissimilatory Nitrate Reduction to Ammonium in the Yellow River Estuary: Rates, Abundance, and Community Diversity – Cuina Bu – Scientific Reports

Built environment
Phage-host associations in a full-scale activated sludge plant during sludge bulking – Ruyin Liu – Applied Microbiology and Biotechnology

Phages and viruses
Metagenomic Analysis of Dairy Bacteriophages: Extraction Method and Pilot Study on Whey Samples Derived from Using Undefined and Defined Mesophilic Starter Cultures – Veronica Barragan – Applied and Environmental Microbiology

Microbes in the news
Flesh-Eating Vibrio Can Come From Cleaning Fish…As Well As Swimming – Judy Stone – Forbes

Burp! Singapore scientists hope for probiotic beer hit – Reuters – Deccan Chronicle

Bacteria Hysteria
Blowing out birthday candles increases bacteria on cake’s icing – study –
Daily Mail

Deadly mix: Brewing faecal bacteria in your coffee cup? – Jagruti Verma – Deccan Chronicle

July 30, 2017

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Relax into your Sunday and read through the days new microbiome research

 

Events and jobs

Laboratory Technician-Microbiology – Wilmington, DE

Pregnancy and early life

Maternal modifiers of the infant gut microbiota: metabolic consequences – Christopher M Mulligan – Journal of Endocrinology

Human respiratory microbiome

Composition and abundance of microbiota in the pharynx in patients with laryngeal carcinoma and vocal cord polyps – Hongli Gong – Journal of Microbiology

Human gut microbiome

Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis – Chengping Wen – Genome Biology

Persistent diarrhea: A persistent infection with enteropathogens or a gut commensal dysbiosis? – Shafiqul A. Sarker – Environmental Microbiology

Reproducibility of assessing fecal microbiota in chronic constipation – G. Parthasarathy – Neurogastroenterology & Motility

Effects of mushroom consumption on the microbiota of different target groups – Impact of polyphenolic composition and mitigation on the microbiome fingerprint – Emanuel Vamanu – LWT – Food Science and Technology

Shotgun metagenomic data on the human stool samples to characterize shifts of the gut microbial profile after the Helicobacter pylori eradication therapy – Eugenia A. Boulygina – Data in Brief

Review: Strategies to increase the efficacy of using gut microbiota for the modulation of obesity – J. Li – Obesity Reviews

Animal experiments 

Amino acid metabolic signaling influences Aedes aegypti midgut microbiome variability – Sarah M. Short – PLOS One

Differential intestinal anti-inflammatory effects of Lactobacillus fermentum and Lactobacillus salivarius in DSS mouse colitis: impact on microRNAs expression and microbiota composition – Alba Rodríguez-Nogales – Molecular Nutrition & Food Research

Animal microbiome

Links between Natural Variation in the Microbiome and Host Fitness in Wild Mammals – Taichi A. Suzuki – Integrative and Comparative Biology

Captivity Shapes the Gut Microbiota of Andean Bears: Insights into Health Surveillance – Andrea Borbón-García – Frontiers in Microbiology

Microbiomes of American Oysters (Crassostrea virginica) Harvested from Two Sites in the Chesapeake Bay – Sylvia Ossai – Genome Announcements

Rumen Microbiome, Probiotics, and Fermentation Additives – Joshua C. McCann – Veterinary Clinics of North America: Food Animal Practice

Plant, root, and soil microbiome

Assessing the influence of farm fertility amendments, field management, and sorghum genotypes on soil microbial communities and grain quality – Adam B. Cobb – Applied Soil Ecology

Rhizospheric Microbiome Profiling of Capsicum annuum L. Cultivated in Amended Soils by 16S and Internal Transcribed Spacer 2 rRNA Amplicon Metagenome Sequencing – Ali Asaff-Torres – Genome Announcements

Peaks of in situ N2O emissions are influenced by N2O producing and reducing microbial communities across arable soils – L.A Domeignoz-Horta – Global Change Biology

Eelgrass Leaf Surface Microbiomes Are Locally Variable and Highly Correlated with Epibiotic Eukaryotes – Mia M. Bengtsson – Frontiers in Microbiology

Microbial community structure is affected by cropping sequences and poultry litter under long-term no-tillage – A.J. Ashworth – Soil Biology and Biochemistry

Interaction of microorganisms within leafy green phyllospheres: Where do human noroviruses fit in? – Wenjun Deng – International Journal of Food Microbiology

Water and extremophile microbiome

Spatial and Temporal Microbial Patterns in a Tropical Macrotidal Estuary Subject to Urbanization – Mirjam Kaestli – Frontiers in Microbiology

Evidence of microbial rhodopsins in Antarctic Dry Valley edaphic systems – Leandro D. Guerrero – Environmental Microbiology

Prokaryotic diversity and community composition in the Salar de Uyuni, a large scale, chaotropic salt flat – Sergio S. Rubin – Environmental Microbiology

Fate of antibiotic resistance genes and their associations with bacterial community in livestock breeding wastewater and its receiving river water – Shuyu Jia – Water Research

Performance and microbial community analysis of a microaerophilic sulfate and nitrate co-reduction system – Xi-Jun Xu – Chemical Engineering Journal

Characteristics of microbial community functional structure of a biological coking wastewater treatment system – Dev Raj Joshi – Journal of Environmental Sciences

Food microbiology

Evolution of microbial community and chemical properties of a sourdough during the production of Colomba, an Italian sweet leavened baked product – Stefano Raimondi – LWT – Food Science and Technology

Bacterial community diversity of traditional fermented vegetables in China – Daqun Liu – LWT – Food Science and Technology