Category Archives: Human skin

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 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

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 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

 

July 23, 2017

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General microbiome

Systems biology of lactic acid bacteria: For food and thought – Bas Teusink, Current Opinion in Systems Biology

Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta) – Susan H. Brawley, PNAS

Parasite Microbiome Project: Systematic Investigation of Microbiome Dynamics within and across Parasite-Host Interactions – Nolwenn M. Dheilly, mSystems

Human respiratory microbiome

Airway microbiota signals anabolic and catabolic remodeling in the transplanted lung – Stéphane Mouraux, Journal of Allergy and Clinical Immunology

Human skin microbiome

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

Human oral microbiome

Metabolic Fingerprints from the Human Oral Microbiome Reveal a Vast Knowledge Gap of Secreted Small Peptidic Molecules – Anna Edlund, mSystems

Human gut microbiome

Sequencing the gut metagenome as a non-invasive diagnosis for advanced nonalcoholic steatohepatitis – Lixin Zhu, Hepatology

Molecular Characterization of the Human Stomach Microbiota in Gastric Cancer Patients – Guoqin Yu, Frontiers in Microbiology

Inulin-type fructans and whey protein both modulate appetite but only fructans alter gut microbiota in adults with overweight/obesity: a randomized controlled trial – Raylene A. Reimer, Molecular Research and Food Research

Incomplete metabolism of phytoestrogens by gut microbiota from children under the age of three – Pilar Gaya, International Journal of Food Sciences and Nutrition

Animal experiments

An In Vitro Chicken Gut Model Demonstrates Transfer of a Multidrug Resistance Plasmid from Salmonella to Commensal Escherichia coli – Roderick M. Card, mBio

Maternally-transmitted microbiota affects odor emission and preference in Drosophila larva – Jean-Pierre Farine, Scientific Reports

Burn Injury Leads to Increase in Relative Abundance of Opportunistic Pathogens in the Rat Gastrointestinal Microbiome – Guangtao Huang, Scientific Reports

Linking Sex Differences in Non-Alcoholic Fatty Liver Disease to Bile Acid Signaling, Gut Microbiota, and High Fat Diet  – John Y.L. Chiang, The American Journal of Pathology

Early-life disruption of amphibian microbiota decreases later-life resistance to parasites – Sarah A. Knutie, Nature Communication

In vitro characteristics of an Atlantic salmon (Salmo salar L.) hind gut microbial community in relation to different dietary treatments – Kamarul Zaman Zarkasia,  Research in Microbiology

Effects of coconut oil on glycemia, inflammation, and urogenital microbial parameters in female Ossabaw mini-pigs – Annie E. Newell-Fugate, PLoS ONE

Effect of acute ozone exposure on the lung metabolomes of obese and lean mice – Joel Andrew Mathews, PLoS ONE

Animal microbiome

Skin Bacterial Community Reorganization Following Metamorphosis of the Fire-Bellied Toad (Bombina orientalis) – Arnaud Bataille, Microbial Ecology

Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste – Grace Tzun-Wen Shaw, PLoS ONE

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation – Olov Svartström, ISME

Genome Sequences of Two Shewanella spp. Isolated from the Gut of the Sea Cucumber Apostichopus japonicus (Selenka, 1867) – Hyun-Hee Hong, Genome Anouncements

Feather-Degrading Bacteria: Their Biochemical and Genetic Characteristics – Paweł Kowalczyk, Arabian Journal for Science and Engineering

Plant, root, and soil microbiome

The tree species matters: Belowground carbon input and utilization in the myco-rhizosphere – Janine Sommera, European Journal of Soil Biology

Soil bacterial community response to vegetation succession after fencing in the grassland of China – Quanchao Zeng, Science of The Total Environment

Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes – Christian Santos-Medellín, mBio

Improved grain yield of cowpea (Vigna unguiculata) under water deficit after inoculation with Bradyrhizobium elkaniiand Rhizophagus irregularis – Rui S. Oliveira, Crop and Pasture Science

Understanding the holobiont: the interdependence of plants and their microbiome – Carmen Sánchez-Cañizares, Current Opinion in Microbiology

Pseudomonas fluorescens R68 assisted enhancement in growth and fertilizer utilization of Amaranthus tricolor (L.) – C. Jimtha John, 3Biotech

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa – Deidré A. B. van Wyk, Journal of Basic Microbiology

A genomic perspective on stoichiometric regulation of soil carbon cycling – Wyatt H Hartman, ISME

The rhizosphere microbiome of burned holm-oak: potential role of the genus Arthrobacter in the recovery of burned soils – Antonio J. Fernández-González, Scientific Reports

Biological control of potential antagonistic bacteria isolates to restrict Magnaporthe grisea infection on rice – David P. Tokpah, African Journal of Microbiology Research

Bacteria associated to plants naturally selected in a historical PCB polluted soil show potential to sustain natural attenuation – Lorenzo Vergani, Frontiers in Microbiology

Water and extremophile microbiome

Unraveling the Microbial Interactions and Metabolic Potentials in Pre- and Post-treated Sludge from a Wastewater Treatment Plant Using Metagenomic Studies – Chandni Sidhu, Frontiers in Microbiology

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

Microbial Community Structure and Function Decoupling Across a Phosphorus Gradient in Streams – Erick S. LeBrun, Microbial Ecology

Microbial communities and their predicted metabolic functions in growth laminae of a unique large conical mat from Lake Untersee, East Antarctica – Hyunmin Koo, Frontiers in Microbiology

Draft genome sequence of Exiguobacterium aurantiacumstrain PN47 isolate from saline ponds, known as “Salar del Huasco”, located in the Altiplano in the North of Chile – Erwin Strahsburger, Brazilian Journal of Microbiology

Diversity of culturable filamentous Ascomycetes in the eastern South Pacific Ocean off Chile – Jeanett Vera, World Journal of Microbiology and Biotechnology

Salinity Drives the Virioplankton Abundance but Not Production in Tropical Coastal Lagoons – Pedro C. Junger, Microbial Ecology

Characterization of a cold-adapted DNA photolyase from C. psychrerythraea 34H – Sudipto Munshi, Extremophiles

Marine archaeal dynamics and interactions with the microbial community over 5 years from surface to seafloor – Alma E Parada, ISME

Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars – Shino Suzuki, ISME

Comparative Omics and Trait Analyses of Marine Pseudoalteromonas Phages Advance the Phage OTU Concept – Melissa B. Duhaime, Frontier in Microbiology

Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs – Chia S. Chan, Frontiers in Microbiology

Climate oscillations reflected within the microbiome of Arabian Sea sediments – William D. Orsi, Scientific Reports

Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre – Mary R. Gradoville, Frontiers in Microbiology

Antarctic sea ice region as a source of biogenic organic nitrogen in aerosols – Manuel Dall’Osto, Scientific Reports

Built environment

A role for microbial selection in frescoes’ deterioration in Tomba degli Scudi in Tarquinia, Italy – Maria Cristina Tomassetti, Scientific Reports

Food microbiology

An Exploration into the Bacterial Community under Different Pasteurization Conditions during Substrate Preparation (Composting–Phase II) for Agaricus bisporus Cultivation – Fabricio Rocha Vieira, Microbial Ecology

Metagenome-based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments – Conor J Doyle, Environmental Microbiology

Draft Genome Sequences of Three Lactobacillusparacasei Strains, Members of the Nonstarter Microbiota of Mature Cheddar Cheese – Ewelina Stefanovic, Genome Anouncements

Bioinformatics

Cohesion: a method for quantifying the connectivity of microbial communities – Cristina M Herren, ISME

Developing integrative systematics in the informatics and genomic era, and calling for a global Biodiversity Cyberbank – Jun Wen, Journal of Systematics and Evolution

Techniques

Rapid differentiation of bacterial communities using high resolution melting analysis – Steven Everman, Journal of Microbiological Methods

Proteomics in Inflammatory Bowel Disease: Approach Using Animal Models – Fadi H. Mourad, Digestive Diseases and Sciences

July 18, 2017

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A short Digest today, but with very interesting papers. Strain diversity implicated in atopic dermatitis, infant gut microbiome associated with cognitive development? And the sourdough microbiome.

General microbiology

Use of oxygen isotopes to differentiate between nitrous oxide produced by fungi or bacteria during denitrification – Lena Rohe et al. – Rapid Communications in Mass Spectrometry

Human skin microbiome

Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis – Allyson Byrd et al. – Science Translational Medicine

Human gut-microbiome-brain axis

Infant Gut Microbiome Associated with Cognitive Development – Alexander L. Carlson et al. – Biological Psychiatry

Press: In baby’s dirty diapers, the clues to baby’s brain development – UNC Health Care – EurekaAlert

Animal experiments

Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring – Jun Miyoshi et al. – Cell Reports

Press: Higher IBD Risk in Offspring Associated With Antibiotic Use in Pregnancy – IDSE News Staff – IDSE

Microbes in the news

More Than Bread: Sourdough As a Window Into The Microbiome – Marcus Woo – NPR

Promising but take caution: Probiotics and Weight Loss – Philip J. Gregory – Medscape

Review article discusses potential role, benefits of non-rhizobia bacteria in root nodules of legume – Phys.org

Microbes on the market

Enterome, Nestlé Health Science Launch Microbiome Diagnostics Partners to Develop New IBD Treatments – Carolina Henriques – IBD News Today

Essential Science: Big investments for human microbiome research – Tim Sandle – Digital Journal

17, July 2017

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In today’s digest, we learn more about how cloud-based computing is making it easier to analyses big datasets, and stochastic bottlenecks control bacterial colonization in animal host.

General Microbiome and Microbiology

New perspectives on dandruff and seborrheic dermatitis: lessons we learned from bacterial and fungal skin microbiota.

Paulino LC. European journal of dermatology

Harnessing microbiome‐based biotechnologies for sustainable mitigation of nitrous oxide emissions

Hu HW.Microbial Biotechnology

Human gut microbiome

Comparisons of Gut Microbiota Among Healthy Control, Patients With Conventional Adenoma, Sessile Serrated Adenoma, and Colorectal Cancer. Yoon H. Journal of Cancer Prevention

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life. Xiong W. Microbiome

Assessing the impact of protein extraction methods for human gut metaproteomics

Zhang  X.Journal of Proteomics

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls

Stewart CJ. Microbiome

Animal and insect microbiome

Host–Microbe Interactions: Winning the Colonization Lottery

Lazzaro BP and GM Fox. Current Biology

Strategies for managing rival bacterial communities: lessons from burying beetles.

Kilner RM. Journal of Animal Ecology

Changes in the Gut Microbial Communities Following Addition of Walnuts to the Diet. Byerley, LO. Journal of Nutritional Biochemistry

Microbiome modelling

The Microbiome and Big Data

Navas-Molina JA. Current Opinion in Systems Biology

Plant, soil, and air microbiome

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US.

Kaleita AL.PloS one

Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata

Zhao M. Applied Soil Ecology

Changes in microbial community composition following phytostabilization of an extremely acidic Cu mine tailings

Yang T. Soil Biology and Biochemistry

Effects of between‐site variation in soil microbial communities and plant‐soil feedbacks on the productivity and composition of plant communities.   Bauer JT.Journal of Applied Ecology

Response of soil microbial communities to elevated antimony and arsenic contamination indicates the relationship between the innate microbiota and contaminant fractions. Sun W. Environmental Science and Technology

Marine and inland waters

The contribution of microbial biotechnology to mitigating coral reef degradation Damjanovic. Microbial Biotechnology

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

Slaby BM. The ISME Journal

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

He T.  mBio

Built Microbiome

Microbial communities on painted wet and dry external surfaces of a historic fortress in Niterói, Brazil. Ogawa A. Journal of International Biodeterioration & Biodegradation

Preprint

Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity.Gerth M.PeerJ

July 7, 2017

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Human Microbiome

Review: Altered molecular signature of intestinal microbiota in irritable bowel syndrome patients compared with healthy controls: A systematic review and meta-analysis – Liu et al. – Digestive and Liver Disease

Non-antibiotic Isotretinoin treatment differentially controls Propionibacterium acnes on skin of acne patients. – Ryan-Kewley et al. – Frontiers in Microbiology

Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy – Namasivayam et al. – Microbiome (BMC)

Research Highlights: Obesity: Gut microbiome and serum metabolome changes – Claire Greenhill – Nature Reviews Endocrinology

Research Highlights:  Gut microbiota: Link between the gut and adipose tissues – Alan Morris – Nature Reviews Endocrinology

Review: The gut microbiome and liver cancer: mechanisms and clinical translation – Yu & Schwabe – Nature Reviews Gastroenterology and Hepatology

 

Pathogens

Reactive Oxygen Species-Dependent Essential Genes in Salmonella Typhimurium – Karash and Min Kwon – BioRxiv

Whole transcriptome sequencing of Pseudomonas syringae pv. actinidiae-infected kiwifruit plants reveals species-specific interaction between long non-coding RNA and coding genes – Wang et al – Scientific Reports (Nature)

Effects of different substrates/growth media on microbial community of saliva-derived biofilm – Li et al – FEMS Microbiology letters

 

Methods (including bioinformatics)

Selective imaging of Gram-negative and Gram-positive microbiotas in the mouse gut – Wang et al. – Biochemistry (ACS)

Methodology: VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data – Ren et al. – Microbiome (BMC)

Methodology: A novel ultra high-throughput 16S rRNA gene amplicon sequencing library preparation method for the Illumina HiSeq platform – de Muinck et al. – Microbiome (BMC)

Completing bacterial genome assemblies with multiplex MinION sequencing – Wick et al. – BioRxiv

Axe: rapid, competitive sequence read demultiplexing using a trie – Murray & Borevitz – BioRxiv

 

Water microbiome

Unraveling the microbial interactions and metabolic potentials in pre- and post-treated sludge from a wastewater treatment plant using metagenomic studies – Sidhu et al. – Frontiers in Microbiology

Nutrient dynamics and stream order influence microbial community patterns along a 2914 km transect of the Mississippi River – Henson et al. – BioRxiv

 

Extremophiles

Oxidative weathering and microbial diversity of an inactive seafloor hydrothermal sulfide chimney – Li et al. – Frontiers in Microbiology

Hidden biofilms in a far northern lake and implications for the changing Arctic – Mohit et al. – npj Biofilms and Microbiomes

 

Probiotics – Fermented Food

Amplicon sequencing of the slpH locus permits culture-independent strain typing of Lactobacillus helveticus in dairy products – Moser et al. – Frontiers in Microbiology

Probiotic Enterococcus mundtii Isolate Protects the Model Insect Tribolium castaneum against Bacillus thuringiensis – Grau et al. – Frontiers in Microbiology

 

Animal Microbiome

Regulation of gut luminal serotonin by commensal microbiota in mice –  Hata et al. – PLoS ONE

 

News

News: How Gut Bacteria Tell Their Hosts What to Eat – Knvul Sheikh via Scientific American Mind (Nature)

News: Mind over Meal: Does Weight-Loss Surgery Rewire Gut-Brain Connections? – Bret Stetka via Scientific American Mind (Nature)

 

Fellowships

Post-Doctoral Research Fellow, Microbiome and Vaccine Induced Immunity – Seattle, WA, United States

Postdoctoral Fellow (Listeria monocytogenes research) – Dunedin, New Zealand

 

Other

The earth is flat (p > 0.05): significance thresholds and the crisis of unreplicable research – Amrhein et al. – PeerJ