November 30, 2018

Happy Friday! Today’s digest features the skin microbiome of lizards and frogs, bacterial changes during palm wine fermentation, and the impact of deforestation on soils in the Amazon.

General microbiome

Review: The microbiome in threatened species conservation – West – Biological Conservation

Human oral microbiome

Oxidative stress in the oral cavity is driven by individual-specific bacterial communities – Džunková – NPJ Biofilms and Microbiomes

Human gut microbiome

Alterations of the gut microbiome and plasma proteome in Chinese patients with adolescent idiopathic scoliosis – Shen – Bone

Animal experiments

Effect of gastric fluid aspiration on the lung microbiota of laboratory rats – Finn – Experimental Lung Research

Animal microbiome

Skin bacterial diversity is higher on lizards than sympatric frogs in tropical Australia – Weitzman – PeerJ

Impact of Bacillus spp. spores and gentamicin on the gastrointestinal microbiota of suckling and newly weaned piglets – Poulsen – PLoS One

Plant, root, and soil microbiome

Land Use Influences Antibiotic Resistance in the Microbiome of Soil Collembolans Orchesellides sinensis – Zhu – Environmental Science and Technology

Deforestation Impacts Network Co-occurrence Patterns of Microbial Communities in Amazon Soils – Khan – FEMS Microbiology Ecology

Review: VOCs-mediated hormonal signaling and crosstalk with plant growth promoting microbes – Tyagi – Critical Reviews in Biotechnology

Soil amendment alters soil physicochemical properties and bacterial community structure of a replanted apple orchard – Liang – Microbiological Research

Specialisation events of fungal metacommunities exposed to a persistent organic pollutant are suggestive of augmented pathogenic potential – Martins – Microbiome

Extemophile microbiome

Salino-alkaline lime of anthropogenic origin a reservoir of diverse microbial communities – Kalwasińska – Science of the Total Environment

Food microbiology

Preprint: Bacterial diversity and population dynamics during the fermentation of palm wine from Guerrero Mexico – Astudillo-Melgar – BioRxiv

Assessment of biogas production and microbial ecology in a high solid anaerobic digestion of major California food processing residues – Achmon – Bioresource Technology Reports

Science, publishing, and career

Preprint: Participation and Motivations of Grant Peer Reviewers: A Comprehensive Survey of the Biomedical Research Community – Gallo – BioRxiv

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October 24, 2018

General Microbiome

REVIEW:Leaky Gut, Leaky Brain? Obrenovich MEM. Microorganisms.

Oral microbiota dysbiosis and its association with Henoch-Schönlein Purpura in children.Chen B. International Immunopharmacology.

Airway microbiome is associated with respiratory functions and responses to ambient particulate matter exposure.Wang L. Ecotoxicology and Environmental Safety

Gut Microbiome

Association of serum bilirubin in newborns affected by jaundice with gut microbiota dysbiosis.Zhou S. The Journal of Nutritional Biochemistry

Author Correction: Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome. Zhernakova DV. Nature Genetics

Competitive lottery-based assembly of selected clades in the human gut microbiome.Verster AJ. Microbiome.

Vaginal Microbiome

Association of cervical microbial community with persistence, clearance and negativity of Human Papillomavirus in Korean women: a longitudinal study.Arokiyaraj S. Scientific Reports

Increased transferrin saturation is associated with subgingival microbiota dysbiosis and severe periodontitis in genetic haemochromatosis.Boyer E. Scientific Reports

Plant, Soil, and Water Microbiome

Regulation of coastal methane sinks by a structured gradient of microbial methane oxidizers.He Z. Environmental Pollution

Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters.Deja-Sikora E. Microbial Ecology

The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales.Li HY. Microbiome

Potential methane production and molecular characterization of bacterial and archaeal communities in a horizontal subsurface flow constructed wetland under cold and warm seasons. López D. The Science of the Total Environments

Biotechnological potential of plant growth-promoting bacteria from the roots and rhizospheres of endemic plants in ironstone vegetation in southeastern Brazil.Felestrino ÉB. World Journal of Microbiology and Biotechnology

Temporal shifts in endophyte bacterial community composition of sessile oak (<i>Quercus petraea</i>) are linked to foliar nitrogen, stomatal length, and herbivory. Borruso L. Peer

Shifts in community composition and co-occurrence patterns of phyllosphere fungi inhabiting <i>Mussaenda shikokiana</i> along an elevation gradient.Qian X. PeerJ.

Techniques

Protocol for faecal microbiota transplantation in ulcerative colitis (FMTUC): a randomised feasibility study.Jitsumura M. BMJ Open

September 20, 2018

Today’s digest presents reviews covering potential of microbiome in olfactory communication and oral-gut microbiome axis in rheumatoid arthritis; articles on association of human gut microbiome with different diseases; news on antibiotics and scientific data on personality types in humans.

General microbiome

Review: The Extended Genotype: Microbially Mediated Olfactory Communication – Alexandra J.R. Carthey – Trends in Ecology and Evolution

Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis – Marines du Teil Espina – FEMS Microbiology Reviews

Commmentary: Regulating stool for microbiota transplantation – Pilar N Ossorio – Gut microbes

Proteomics and the microbiome: pitfalls and potential – Huafeng Lin – Expert Review of Proteomics

Pregnancy and early life

Postnatal exposure to household disinfectants, infant gut microbiota and subsequent risk of overweight in children – Mon H. Tun – Canadian Medical Association Journal

Human gut microbiome

Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes, MODY2, and Healthy Control Subjects: A Case-Control Study – Isabel Leiva-Gea – Diabetes Care

Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China – Mengxiang Zhang – Scientific Reports

Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer – Marta Mangifesta – Scientific Reports

Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation – Christopher Staley – Microbiome

Could fecal phenylacetic and phenylpropionic acids be used as indicators of health status? – Isabel Gutiérrez-Díaz – Journal of Agricultural and Food Chemisty

Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation – Sean M. P. Bennet – Neurogastroenterology and Motility

Animal experiments

Melatonin reprogramming of gut microbiota improves lipid dysmetabolism in high fat diet-fed mice – Jie Yin – Journal of Pineal Research

Water and extremophile microbiome

Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake – Keith Arora-Williams – Microbiome

Probiotics/Prebiotics

The Impact of Probiotic Supplements on Cognitive Parameters in Euthymic Individuals with Bipolar Disorder: A Pilot Study – Eva Z Reininghaus – Neuropsychobiology

Microbes in the news

The case for expensive antibioticshttp://www.wired.com

Crucial antibiotics still used on US farms despite public health fear  The Guardian

Non-microbiology picks

A robust data-driven approach identifies four personality types across four large data sets – Martin Gerlach – Nature Human Behaviour

 

November 1, 2017

Happy November everybody! We have an interesting collection of articles today. Co-cultivation of plant beneficial fungi as an effective strategy to modulate the production of bioactive metabolites and a review on the benefits of berries and their phytochemicals on the digestive and immune systems. Enjoy!

Events and jobs

Microbiology Lab Assistant – Seattle, Washington – Labcorp

General microbiome

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study – Hemmings, Sian M.J – Pyschosomatic Medicine

Human respiratory microbiome

Review : CF Airway Microbiome: Overturning the Old, Opening the Way for the New – George A. O’Toole – Journal of Bacteriology

Human oral microbiome

Effect of maltitol-containing chewing gum use on the composition of dental plaque microbiota in subjects with active dental caries – Erica M. Prosdocimi – Journal of Oral Microbiology

Human gut microbiome

The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis – Puneet Puri – Hepatology

Diet, Environments, and Gut Microbiota. A Preliminary Investigation in Children Living in Rural and Urban Burkina Faso and Italy – Carlotta De Filippo – Frontiers in Microbiology

Gut microbiome of mothers delivering prematurely shows reduced diversity and lower relative abundance of Bifidobacterium and Streptococcus – Cecilie Dahl – Plos One

Review : Systematic review of the effects of the intestinal microbiota on selected nutrients and non-nutrient – Colette Shortt – European Journal of Nutrition

Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro – Hasinika K. A. H. Gamage – Scientific Reports

Animal experiments

Antibiotic treatment disrupts bacterial communities in the colon and rectum of SIV-infected macaques – Alexander S. Zevin – FEMS Microbiology Letters

Ophiopogonin D alleviates high-fat diet–induced metabolic syndrome and changes the structure of gut microbiota in mice – Siyu Chen – The FASEB Journal

Animal microbiome

Bacterial Species Identified on the Skin of Bottlenose Dolphins Off Southern California via Next Generation Sequencing Techniques – Corey D. Russo – Microbial Ecology

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits – Ara S. Winter – PeerJ

Analysis of the Microbial Diversity in the Fecal Material of Giraffes – Jessica M. Schmidt – Current Microbiology

Morphological and genetic factors shape the microbiome of a seabird species (Oceanodroma leucorhoa) more than environmental and social factors – Douglas S. Pearce – Microbiome

Metabolomics

Plasma Metabolites From Choline Pathway and Risk of Cardiovascular Disease in the PREDIMED (Prevention With Mediterranean Diet) Study – Marta Guasch-Ferré – Journal of the American Heart Association

Plant, root, and soil microbiome

Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia – Manoj Kumar – Frontiers in Microbiology

An endophytic Bacillus strain promotes growth of oil palm seedling by fine root biofilm formation – MdHoirul Azri – Rhizosphere

Effect of auxin producing and phosphate solubilizing bacteria on mobility of soil phosphorus, growth rate, and P acquisition by wheat plants – Guzel R. Kudoyarova – Acta Physiologiae Plantarum

Contrasting effects of ammonium and nitrate additions on the biomass of soil microbial communities and enzyme activities in subtropical China – Chuang Zhang – Biogeosciences

Impact of land use change and soil organic carbon quality on microbial diversity in soils across Europe – Márton Szoboszlay – FEMS Microbiology Ecology

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea – Yu Zhang – Frontiers in Microbiology

Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens – Cara H. Haney – Molecular Ecology

*Co-Culture of Plant Beneficial Microbes as Source of Bioactive Metabolites – F. Vinale – Scientific Reports

Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database – Andrew Bissett – Gigascience

Water and extremophile microbiome

Anaerobic digestion of spent mushroom substrate under thermophilic conditions: performance and microbial community analysis – Zheng Xiao – Applied Microbiology and Biotechnology

Metagenomic characterization of biofilter microbial communities in a full-scale drinking water treatment plant – Seungdae Oh – Water Research

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau – Yong-Liang Chen – Molecular Ecology

Community composition and assembly processes of the free-living and particle-attached bacteria in Taihu Lake – Dayong Zhao – FEMS Microbiology Ecology

Food Microbiology

Anti-obesity Effect of Exopolysaccharides Isolated from Kefir Grains – Juha Lim – J. Agric. Food Chem

Modulating Effects of Dicaffeoylquinic Acids from Ilex Kudingcha on Intestinal Microecology in vitro – Minhao Xie – Journal of Agricultural Food Chemistry

*Review of the health effects of berries and their phytochemicals on the digestive and immune systems – Coen Govers – Nutrition Reviews

Probiotics / prebiotics

Single-species versus dual-species probiotic supplementation as an emerging therapeutic strategy for obesity – G.Karimi – Nutrition, Metabolism and Cardiovascular Diseases

Bioinformatics

ROCker: accurate detection and quantification of target genes in short-read metagenomic data sets by modeling sliding-window bitscores – Luis H. Orellana – Nucleic Acids Research

Phages and viruses

Review : Assessing Species Diversity Using Metavirome Data: Methods and Challenges – Damayanthi Herath – Computational and Structural Biotechnology Journal

Microbes in the news

Caves Host Gooey Biofilms Built by Methane-Eating Bacteria

3D Printed Artificial Small Intestine to Advance Research on Gut Bacteria

Enzymes from dangerous bacteria turn into important tools for protein chemistry

Microbes on the market

The University Medical Center Groningen and Novogene announce the start of the 10K Metagenome Project

Science, publishing, and career

Book Chapter : Leading Change in Undergraduate STEM Education – Adam K. Leibovich – Educational and Outreach Projects from the Cottrell Scholars Collaborative Undergraduate and Graduate Education Volume 1

Anitha’s non-microbiology picks

Congratulations Nancy Scherich! The winner of this year’s ‘Dance Your Ph.D.’ contest

ROSINA spectral measurements bring comet’s chemistry to life

Scary as they are, few vampires have a backbone

 

October 24, 2018

Today’s digest is full of REALLY cool science and features including a 3D image of the human lung microbiome and metabolome, how gut microbiome of wild mice promotes fitness, and an interesting perspective piece on how environmental filtering applies to microbiomes.

General microbiome

Environmental Filtering Is a Relic. A Response to Cadotte and Tucker.

Aguilar-Trigueros CA- Trends in Ecology and Evolution

Gut microbiome

The Leaky Gut and Altered Microbiome in Chronic Kidney Disease.

Lau WL- Journal of Renal Nutrition

Linking the Gut Microbial Ecosystem with the Environment: Does Gut Health Depend on Where We Live?

Tasnim N- Frontiers in Microbiology

Skin microbiome

High-Altitude Living Shapes the Skin Microbiome in Humans and Pigs.

Zeng B- Frontiers in Microbiology

Lung microbiome

Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung

Garg N- Cell Host and Microbe

Animal microbiome

Wild Mouse Gut Microbiota Promotes Host Fitness and Improves Disease Resistance

Rosshart SP- Cell

Plant and soil microbiome

Soil bacterial community mediates the effect of plant material on methanogenic decomposition of soil organic matter

Yuan Q- Soil Biology and Biochemistry

Bacterial communities in soil become sensitive to drought under intensive grazing

Jurburg SD- Science of the Total Environment

Prokaryotic Community Distribution along an Ecological Gradient of Salinity in Surface and Subsurface Saline Soils.

Xie K- Scientific reports

Marine and inland water microbiome

Transcriptional activities of the microbial consortium living with the marine nitrogen-fixing cyanobacterium Trichodesmium reveal potential roles in community-level nitrogen cycling

Lee MD-Applied and Environmental Microbiology

Dynamic microbial populations along the Cuyahoga River.

Cannon MV-  PloS one

Preprint

High degree of virulence gene diversity in Streptococcus pyogenes isolated in Central Italy

Bencardino D- BioRxiv

Microbiome News

I Wish I’d Known This Before I Gave Birth

-mindbodygreen.com

August 3, 2017

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

July 26, 2017

General microbiome

Microbiome analysis and confocal microscopy of used kitchen sponges reveal massive colonization by Acinetobacter, Moraxella and Chryseobacterium species – Massimiliano Cardinale – Scientific Reports

Review: The mother–offspring dyad: microbial transmission, immune interactions and allergy development – Maria C. Jenmalm – Journal of Internal Medicine

Human skin microbiome

The Skin Microbiome of Cohabiting Couples – Ashley A. Ross – mSystems

Animal microbiome

Influence of Host Plant on Thaumetopoea pityocampa Gut Bacterial Community – Cinzia P. Strano – Microbial Ecology

The time-course of broiler intestinal microbiota development after administration of cecal contents to incubating eggs – Erin E. Donaldson – PeerJ

Plant, root, and soil microbiome

Review: Sphingomonads in Microbe-Assisted Phytoremediation: Tackling Soil Pollution – Michael Gatheru Waigi – Trends in Biotechnology

Response of soil microbial community composition and function to a bottomland forest restoration intensity gradient – Michael S. Strickland – Applied Soil Ecology

Changes of soil microbial communities during decomposition of straw residues under different land uses – Hong Zhang – Journal of Arid Land

Water and extremophile microbiome

Metagenomics of urban sewage identifies an extensively shared antibiotic resistome in China – Jian-Qiang Su – Microbiome

An anaerobic ~3400 Ma shallow-water microbial consortium: presumptive evidence of Earth’s Paleoarchean anoxic atmosphere – J. William Schopf – Precambrian Research

Iron oxides alter methanogenic pathways of acetate in production water of high-temperature petroleum reservoir – Pan Pan – Applied Microbiology and Biotechnology

Food Microbiology

Editorial: Microbiology of Ethnic Fermented Foods and Alcoholic Beverages of the World – Jyoti P. Tamang – Frontiers in Microbiology

Probiotics / prebiotics

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74 – Roberto Berni Canani – Applied and Environmental Microbiology

Phages and viruses

Review : The Human Virome – Implications for Clinical Practice in Transplantation Medicine – Susanna K. Tan – Journal of Clinical Microbiology

Anitha’s non-microbiology picks

Quantum tunneling takes time, new study shows

Perovskites power up the solar industry

Scientists develop fast chemistry that unlocks a new class of polymers

Medicine’s Movable Feast: What Jumping Genes Can Teach Us about Treating Disease