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

July 29, 2017

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Enjoy perusing this beefy Microbiome Digest, which is heavy on information about plant/root/soil microbes, water/extremophile microbes, and new microbial techniques.

Events and jobs

Microbiome Symposium 2017 – September 11, Quadras Conference Center

General microbiome

Temperature, inocula and substrate: Contrasting electroactive consortia, diversity and performance in microbial fuel cells – E.S. Heidrich, Bioelectrochemistry

Effect of glucose on nitrogen removal and microbial community in anammox-denitrification system – Yujie Qin, Bioresource Technology

Horizontal Gene Transfer and Ecosystem Function Dynamics – Maarten van de Guchte, Trends in Microbiology

Pregnancy and early life

Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective – Isabelle Laforest-Lapointe, Frontiers in Microbiology

Maternal Gut Microbiome Biodiversity in Pregnancy – Marcela C. Smid, American Journal of Perinatology

Sphingolipid metabolism potential in fecal microbiome and bronchiolitis in infants: a case–control study – Kohei Hasegawa, BMC Research Notes

Adverse events in women and children who have received intrapartum antibiotic prophylaxis treatment: a systematic review – Farah Seedat, BMC Pregnancy and Childbirth

Human skin microbiome

Bacterial diversity in Buruli ulcer skin lesions: Challenges in the clinical microbiome analysis of a skin disease – Chloé Van Leuvenhaege, PLoS ONE

Human oral microbiome

16S rDNA analysis of periodontal plaque in chronic obstructive pulmonary disease and periodontitis patients – Wu X., Journal of Oral Microbiology

Porphyromonas gingivalis disturbs host-commensal homeostasis by changing complement function – Olsen I., Journal of Oral Microbiology

Human gut microbiome

The Present Status of Fecal Microbiota Transplantation and Its Value in the Elderly – Yao-Wen Cheng, Current Treatment Options in Gastroenterology

Fecal total iron concentration is inversely associated with fecal Lactobacillus in preschool children – Sasank Kalipatnapu, Gastroenterology

Long-term irritable bowel syndrome symptom control with reintroduction of selected FODMAPs – Ruth M. Harvie, World Journal of Gastroenterology

Distinct gut microbiota profiles in patients with primary sclerosing cholangitis and ulcerative colitis – Lukas Bajer, World Journal of Gastroenterology

Eubiotic properties of rifaximin: Disruption of the traditional concepts in gut microbiota modulation – Francesca Romana Ponziani, World Journal of Gastroenterology

Helicobacter pylori and gut microbiota in multiple sclerosis versus Alzheimer’s disease: 10 pitfalls of microbiome studies – Ah-Mee Park, Clinical and Experimental Neuroimmunology

Partners of patients with ulcerative colitis exhibit a biologically relevant dysbiosis in fecal microbial metacommunities – Guang-Lan Chen, World Journal of Gastroenterology

Animal Experiments

Oral administration of live- or heat-killed Candida albicansworsened cecal ligation and puncture sepsis in a murine model possibly due to an increased serum (1→3)-β-D-glucan – Wimonrat Panpetch, PLoS ONE

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

Animal microbiome

Changes in the Intestinal Microbiota of Gibel Carp (Carassius gibelio) Associated with Cyprinid herpesvirus2 (CyHV-2) Infection – Rong She, Current Microbiology

Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef – Vanessa R. Marcelino, Molecular Ecology

Characterization of feather-degrading bacterial populations from birds’ nests – Potential strains for biomass production for animal feed – Maria Saarela, International Biodeterioration & Biodegradation

The impact of the bovine fecal microbiome on Escherichia coli O157:H7 prevalence and enumeration in naturally infected cattle – Minseok Kim, Journal of Applied Microbiology

Burying beetles regulate the microbiome of carcasses and use it to transmit a core microbiota to their offspring – Shantanu P. Shukla, Molecular Ecology

Plant, root, and soil microbiome

Elevated CO2 and nitrogen addition have minimal influence on the rhizospheric effects of Bothriochloa ischaemum – Lie Xiao, Scientific Reports

Soil nutritional status and biogeography influence rhizosphere microbial communities associated with the invasive tree Acacia dealbata – Casper N. Kamutando, Scientific Reports

Biotoxic impact of heavy metals on growth, oxidative stress and morphological changes in root structure of wheat (Triticum aestivum L.) and stress alleviation by Pseudomonas aeruginosa strain CPSB1 – Asfa Rizvi, Chemosphere

Use of microbial indicators combined with environmental factors coupled to metrology tools for discrimination and classification of Luzhou-flavored pit muds – Q.Y. Zhang, Journal of Applied Microbiology

Fertilization decreases compositional variation of paddy bacterial community across geographical gradient – Ruirui Chen, Soil Biology and Biochemistry

Effects of snow cover plus straw mulching on microorganisms in paddy soil during winter – Hao Zhang, Applied Soil Ecology

The Contribution of Pyrene Degrading Bacteria and Chemical Reagents to Scirpus triqueterPhytoremediation of Pyrene and Ni Co-contaminated Soil – Xiaoxin Hu, Water, Air, & Soil Pollution

Investigating whether light intensity can modify decomposition rates in peatlands through control of the ‘enzymic latch’ – Christian Dunn, Ecological Engineering

Analysis of microbiota in rhizosphere, water and gut of grass carp (Ctenopharyngodon idella) in ponds treated with artificial floating beds – Jian Li, Water and Environment Journal

Scaling from the growth chamber to the greenhouse to the field: Demonstration of diminishing effects of mitigation of salinity in peppers inoculated with plant growth-promoting bacterium and humic acids – Macario Bacilio, Applied Soil Ecology

Disease management of tomato through PGPB: current trends and future perspective – Vipin Kumar Singh, 3 Biotech

Soil bacteria and archaea change rapidly in the first century of Fennoscandian boreal forest development – Stephanie A. Yarwood, Soil Biology and Biochemistry

Leaf litterfall decomposition of pedunculate (Quercus robur L.) and sessile (Q. petraea [Matt.] Liebl.) oaks and their hybrids and its impact on soil microbiota – Girmantė Jurkšienė, Dendrobiology

On the controls of abundance for soil-dwelling organisms on the Tibetan Plateau – Ke Zhao, Ecosphere

Water and extremophile microbiome

Microbial planktonic communities in the Red Sea: high levels of spatial and temporal variability shaped by nutrient availability and turbulence – John K. Pearman, Scientific Reports

Characterization of a highly efficient antibiotic-degrading metallo-β-lactamase obtained from an uncultured member of a permafrost community – Marcelo Monteiro Pedroso, Metallomics

Polycyclic aromatic hydrocarbons (PAHs) enrich their degrading genera and genes in human-impacted aquatic environments – Ke Yuan, Environmental Pollution

Spatial autocorrelation of microbial communities atop a debris-covered glacier is evidence of a supraglacial chronosequence – Jack L. Darcy, FEMS Microbiology Ecology

Eco-friendly and efficient in situ restoration of the constructed sea stream by bioaugmentation of a microbial consortium – Jangyeon Yoo, Korean Journal of Microbiology

Identification of two organohalide-respiring Dehalococcoidiaassociated to different dechlorination activities in PCB-impacted marine sediments – Andrea Nuzzo, Microbial Cell Factories

Draft genome sequence of the halophilic Halobacillus mangroviKTB 131 isolated from Topan salt of the Jeon-nam in Korea – Mingyeong Woo, Genomics Data

First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile – Antonio E. Serrano, Extended Genome Report

Draft Genome Sequence of the Deep-Sea Bacterium Moritella sp. JT01 and Identification of Biotechnologically Relevant Genes – Robert Cardoso de Freitas, Marine Biotechnology

Bacterial and Archaeal Diversity in Hypersaline Cyanobacterial Mats Along a Transect in the Intertidal Flats of the Sultanate of Oman – Janina C. Vogt, Microbial Ecology

Bacterial and fungal communities and contribution of physicochemical factors during cattle farm waste composting – Huhe, Microbiology Open

Built environment

Bioprotection of the built environment and cultural heritage – Geoffrey Michael Gadd, Microbial Biotechnology

Food microbiology

Food waste conversion to microbial polyhydroxyalkanoates – Chad Nielsen, Microbial Biotechnology

Insect frass in stored cereal products as a potential source of Lactobacillus sanfranciscensis for sourdough ecosystem – Federica Boiocchi, Journal of Applied Microbiology

Probiotics

Evaluation of Probiotic Diversity from Soybean (Glycine max) Seeds and Sprouts Using Illumina-Based Sequencing Method – Yali Huang, Probiotics and Antimicrobial Proteins

Bioinformatics

Visibiome: an efficient microbiome search engine based on a scalable, distributed architecture – Syafiq Kamarul Azman, BMC Bioinformatics

Techniques

Inferring Past Environments from Ancient Epigenomes – David Gokhman, Microbial Ecology and Evolution

Comparison of DNA extraction methods used to detect bacterial and yeast DNA from spiked whole blood by real-time PCR – Libera M. Dalla-Costa, Journal of Microbiological Methods

Understanding the fundamental mechanisms of biofilms development and dispersal: BIAM (Biofilm Intensity and Architecture Measurement), a new tool for studying biofilms as a function of their architecture and fluorescence intensity – Marine Baudin, Journal of Microbiological Methods

Comparison of sequencing the D2 region of the large subunit ribosomal RNA gene (MicroSEQ®) versus the internal transcribed spacer (ITS) regions using two public databases for identification of common and uncommon clinically relevant fungal species – S. Arbefeville, Journal of Microbiological Methods

The feasibility of improved live-dead distinction in qPCR-based microbial source tracking – Laura Seidel, Journal of Microbiological Methods

Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica – Hyunmin Koo, Journal of Microbiological Methods

Multiplex polymerase chain reaction for identification of Escherichia coli, Escherichia albertii and Escherichia fergusonii – Rebecca L. Lindsey, Journal of Microbiological Methods

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data – David Paez-Espino, Nature Protocols

SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree – John R. Stevens, Computational and Structural Biotechnology Journal

July 28, 2017

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Microbiome Research

High spatial and temporal variations of microbial community along the southern catfish gastrointestinal tract: insights into dynamic food digestion – Zhimin Zhang – Frontiers in Microbiology

Host ecology rather than host phylogeny drives amphibian skin microbial community structure in the biodiversity hotspot of Madagascar – Molly C. Bletz – Frontiers in Microbiology

A pilot study demonstrating the altered gut microbiota functionality in stable adults with Cystic Fibrosis – F. Fouhy  – Scientific Reports

Research Highlight: Baby bugs can’t stop the thugs… – Yvonne Bordon – Nature Reviews Immunology

Chondroitin sulfate disaccharides modified the structure and function of the murine gut microbiome under healthy and stressed conditions – Fang Liu – Scientific Reports

Nasopharyngeal microbiome in premature infants and stability during rhinovirus infection – Geovanny F Perez – Journal of Investigative Medicine

Microbiomarkers in inflammatory bowel diseases: caveats come with caviar – Felix Sommer – Gut (BMJ)

Kynurenines: Tryptophan’s metabolites in exercise, inflammation, and mental health – Igor Cervenka – Science

 

Probiotics, Prebiotics and bioactive compounds

Protection mechanism of Clostridium butyricum against Salmonella enteritidis infection in broilers – Xiaonan Zhao – Frontiers in Microbiology

Isolation of human intestinal bacteria capable of producing the bioactive metabolite isourolithin A from ellagic acid – Maria V. Selma – Frontiers in Microbiology

Anti-obesity and anti-inflammatory effects of synthetic acetic acid vinegar and Nipa vinegar on high-fat-diet-induced obese mice – Boon Kee Beh – Scientific Reports

Antimicrobial activities of widely consumed herbal teas, alone or in combination with antibiotics: an in vitro study – Mayram Hacioglu – PeerJ

 

Food microbiology

Primary souring: a novel bacteria-free method for sour beer production – Kara Osburn – BioRxiv

 

Bioinformatics

PhaMers identifies novel bacteriophage sequences from thermophilic hot springs – Jonathan Deaton -BioRxiv

PinAPL-Py: A comprehensive web-application for the analysis of CRISPR/Cas9 screens – Philipp N. Spahn – BioRxiv

 

Pathogens

PyroTyping, a novel pyrosequencing-based assay for Mycobacterium tuberculosis genotyping –  B. Molina-Moya – Scientific Reports

Vibrio cholerae genomic diversity within and between patients – Inès Levade – BioRxiv

Experimental evolution and genome data analysis of Candida albicans reveals cryptic bacteria in single yeast colonies – Danielle C. F. Bruno – BioRxiv

Comments and Opinion: The theory of disappearing microbiota and the epidemics of chronic diseases – Martin J. Blaser – Nature Reviews Immunology

Bactericidal and anti-biofilm effects of polyhexamethylene biguanide in models of intracellular and biofilm of Staphylococcus aureus isolated from bovine mastitis -Nor Fadhilah Kamaruzzaman – Frontiers in Microbiology

Clinicians should assess the benefits and risks of using bezlotoxumab for reducing the risk of recurrent Clostridium difficile infection – Habiba Hassouna – Evidence based Medicine

Whole RNA-sequencing and transcriptome assembly of Candida albicans and Candida africana under chlamydospore-inducing conditions – Domenico Giosa – Genome Biology and Evolution

 

Soil/Environmental Microbiome

The rhizosphere bacterial microbiota of Vitis vinifera cv. Pinot Noir in an integrated pest management vineyard – Giorgia Novello – Frontiers in Microbiology

Microbial Community Structure and the Persistence of Cyanobacterial Populations in Salt Crusts of the Hyperarid Atacama Desert from Genome-Resolved Metagenomics – Kari M. Finstad – Frontiers in Microbiology

Long term fertilization structures Bacterial and Archaeal communities along soil depth gradient in a paddy soil – Yunfu Gu – Frontiers in Microbiology

Drought and host selection influence bacterial community dynamics in the grass root microbiome – Dan Naylor – The ISME Journal

 

Other (Non-microbiology picks)

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus – Yuki Yoshida – Plos Biology

 

 

 

July 27, 2017

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General microbiome

Microbiota-host Transgenomic Metabolism, Bioactive Molecules from the Inside –  S Turroni – J. Med. Chem.

Cyanophages exhibit rhythmic infection patterns under light-dark cycles – R Liu – bioRxiv

The effect of aspartate supplementation on the microbial composition and innate immunity on mice – P Bin – Amino Acids

Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation – N Doki – Annals of Hematology

Differentiating botulinum-neurotoxin-producing clostridia with a simple, multiplex PCR assay – CHD Williamson – Appl. Environ. Microbiol.

Review: Antimicrobial resistance in the next 30 years, humankind, bugs and drugs: a visionary approach – M Bassetti – Intensive Care Med.

Lactobacillus fermentum CECT 5716 and a reduction of the Staphylococcus load in breast milk which reduces the risk of infectious mastitis: evaluation of a health claim pursuant to Article 14 of Regulation (EC) No 1924/2006 – EFSA Panel – EFSA Journal

 

Human gut microbiome

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 – R Canani Berni – Appl. Environ. Microbiol.

Examining the gut bacteriome, virome, and mycobiome in glucose metabolism disorders: Are we on the right track? –  C Stefenaki – Metab.Clin.Exp.

 

Animal microbiome

Assessment of Cultivable Oral Bacterial Flora from Important Venomous Snakes of India and Their Antibiotic Susceptibilities – IK Shaikh – Current Microbiology

 

Plant, root and soil microbiome

Rhizosphere Sampling Protocols for Microbiome (16S/18S/ITS rRNA) Library Preparation and Enrichment for the Isolation of Drought Tolerance-Promoting Microbes – V Lakshmanan – Methods in Molecular Biology

Toward a Resilient, Functional Microbiome: Drought Tolerance-Alleviating Microbes for Sustainable Agriculture – V Lakshmanan – Methods in Molecular Biology

Review: Biochar-rhizosphere interactions – A review – S Głuszek – Pol J Microbiol.

Interactions between Pteris vittata L. genotypes and a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium (Alcaligenes sp.) in arsenic uptake and PAH-dissipation – L Sun -Environmental Pollution

 

Built environment

The performance and microbial communities of biodegradation-electron transfer with sulfur metabolism integrated process for flue gas desulfurization wastewater treatment – C Wei – Bioprocess Biosyst Eng.

 

Techniques

Dual RNA-Seq of Lysobacter capsici AZ78 – Phytophthora infestans interaction shows the implementation of attack strategies by the bacterium and unsuccessful oomycete defense responses –  S Tomada – Environmental Microbiology

 

Microbes in news

Infant Gut Microbiome May Influence Cognitive Development – Whole Foods Magazine

HEALTHY BITES: The importance of a healthy gut – My Web Times

Why apartment dwellers need indoor plants – Phys.org

Algae cultivation technique could advance biofuels – Science Daily

Bacteria may explain why uncircumcised face higher HIV risk – UPI

Cafe shut down at LA Fitness that had Legionnaires’ bacteria – Orlando Sentinel

Link between Saharan Dust and Vibrio bacteria – Kiiitv.com

Life evolves adaptions to microgravity – Phys.org

Algal solution- Could Spirulina modify the microbiome to protect against age related damage – Nutra Ingredients

Penis Microbiome Could Enhance Risk of Infection with HIV – Invisiverse

Building Codes for Bacterial Cities – Quanta Magazine

Researchers offer new and novel paradigm for advancing research on beneficial microbes – Phys.org

15 facts about fecal transplants – The straight poop – Genetic Literacy Project

He thought he just had blisters from a hike. He had flesh-eating bacteria and nearly died – The Washington Post

$1.8 million NIH grant to Wayne State to aid in developing improved cholera treatments – EurekAlert

Investigator | High levels of E.Coli bacteria found at local shopping malls – WKYC

Beautiful and bizarre things to buy: From wall art to a probiotic deodorant – Livemint

July 26, 2017

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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

July 25, 2017

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General Microbiome

Correcting for batch effects in case-control microbiome studies – Sean Gibbons – BioRxiv

Richer gut microbiota with distinct metabolic profile in HIV infected Elite Controllers – – Jan Vesterbacka – Scientific Reports (Nature)

Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities – V. Shankar – Scientific Reports (Nature)

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 – Moana Mika – Microbiome (BMC)

Design and validation of a DNA-microarray for phylogenetic analysis of bacterial communities in different oral samples and dental implants – Carola Parolin – Scientific Reports (Nature)

Research Highlight: The innate immune receptor NLRP12 maintains intestinal homeostasis by regulating microbiome diversity – Jenny Moi-Fong Lau and Yvonne Dombrowski – Cellular & Molecular Immunology

Human Milk Microbial Community Structure Is Relatively Stable and Related to Variations in Macronutrient and Micronutrient Intakes in Healthy Lactating Women – Janet E Williams – The Journal of Nutrition

The Brain-Gut Axis Contributes to Neuroprogression in Stress-Related Disorders – Rea K. – Neuroprogression in Psychiatric Disorders

A nutritional approach for managing irritable bowel syndrome – Natalie Bhesania – Current Opinion in Pediatrics

Microbiota, metabolome, and immune alterations in obese mice fed a high fat diet containing type 2 resistant starch – Javad Barouei – Molecular Nutrition and Food Research

Diet Versus Phylogeny: a Comparison of Gut Microbiota in Captive Colobine Monkey Species – Vanessa L. Hale – Microbial ecology

Effects of oral florfenicol and azithromycin on gut microbiota and adipogenesis in mice – Rui Li – PlosOne

 

Probiotics

Review (Provisionally accepted): Bacillus as potential probiotics: status, concerns and future perspectives – Fouad M. F. Elshaghabee – Frontiers in Microbiology

Non-antibiotic Isotretinoin Treatment Differentially Controls Propionibacterium acnes on Skin of Acne Patients – Angela E. Ryan-Kewley – Frontiers in Microbiology

Effect of probiotics on the meat flavour and gut microbiota of chicken – Yan Wang – Scientific Reports (Nature)

 

Pathogens

Minireview: Insight Into the Origin and Evolution of the Vibrio parahaemolyticus Pandemic Strain – Romilio T. Espejo – Frontiers in Microbiology

Nitrate Sensing and Metabolism Inhibit Biofilm Formation in the Opportunistic Pathogen Burkholderia pseudomallei by Reducing the Intracellular Concentration of c-di-GMP – Mihnea R. Mangalea – Frontiers in Microbiology

Trehalose Polyphleates, External Cell Wall Lipids in Mycobacterium abscessus, Are Associated with the Formation of Clumps with Cording Morphology, Which Have Been Associated with Virulence – Marta Llorens-Fons –  Frontiers in Microbiology

The resident pathobiont Staphylococcus xylosus in Nfkbiz-deficient skin accelerates spontaneous skin inflammation – Yeji Kim – Scientific Reports (Nature)

Inactivation Mechanism of Escherichia coli Induced by Slightly Acidic Electrolyzed Water – Zhangying Ye – Scientific Reports (Nature)

Targeting the permeability barrier and peptidoglycan recycling pathways to disarm Pseudomonas aeruginosa against the innate immune system –  Gabriel Torrens – PlosOne

 

Environmental Microbiology

Modified Lipid Extraction Methods for Deep Subsurface Shale  – Rawlings N. Akondi – Frontiers in Microbiology

The Cyanobacteria-Dominated Sponge Dactylospongia elegans in the South China Sea: Prokaryotic Community and Metagenomic Insights – Zhao-Ming Gao – Frontiers in Microbiology

 

Towards a highly efficient diversity census of the prokaryotic biosphere: a group testing approach – Bar Shalem – BioRxiv

Protocol: Rhizosphere Sampling Protocols for Microbiome (16S/18S/ITS rRNA) Library Preparation and Enrichment for the Isolation of Drought Tolerance-Promoting Microbes – Venkatachalam Lakshmanan – Methods in molecular biology

Endophytic fungal communities of Polygonum acuminatum and Aeschynomene fluminensis are influenced by soil mercury contamination – William Pietro-Souza  – PlosOne