July 14, 2018

 

Editorial

Ediorial:The nasal microbiome: opening new clinical research avenues for allergic disease.Mahdavinia M.

Beyond Bacteria: Bacteriophage-Eukaryotic Host Interactions Reveal Emerging Paradigms of Health and Disease.Chatterjee A. Frontiers in Microbiology. Expert Rev Clin Immunol

Correction

Correction:Huddling remodels gut microbiota to reduce energy requirements in a small mammal species during cold exposure.Zhang XY. Microbiome.

General Microbiome

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.Yassour M. Cell Host Microbe

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome.Ferretti P. Cell Host Microbe

Reduced microbiome alpha diversity in young patients with ADHD.Prehn-Kristensen A. PLoS One.

Reducing healthcare-associated infections incidence by a probiotic-based sanitation system: A multicentre, prospective, intervention study. Caselli E. PLoS One

The Microbiome and Pancreatic Cancer: An Evidence-based Association?Archibugi L. Journal of  Clinical Gastroenterology

Testing the light:nutrient hypothesis: Insights into biofilm structure and function using metatranscriptomics.Veach AM. Molecular Ecology

Animal Experiments and Microbiome

Modulation of the honey bee queen microbiota: Effects of early social contact.Powell JE. PLoS One. 2018

Plants, Soil, and Water Microbiome

Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia. Garrido-Oter R

Biodiversity of cultivable Burkholderia species in Argentinean soils under no-till agricultural practices. Draghi WO.  PLoS One

Characterized non-transient microbiota from stinkbug (Nezara viridula) midgut deactivates soybean chemical defenses. Medina V. PLoS One.

Characterization of Actinobacterial Communities from Arauca River Sediments (Colombia) Reveals Antimicrobial Potential Presented in Low Abundant Isolates.Arango C, Open Microbiology Journal. Cell Host Microbe.

Predictive Modeling of Microbiome Data Using a Phylogeny-Regularized Generalized Linear Mixed Model. Xiao J.Frontier in Microbiology

Virome

Characterization of airborne viromes in cheese production plants. Colombo S.Journal of Applied Microbiology

 

 

 

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11 July, 2018

Today’s digest is short but full of exciting research. Firstly, a look at how maternal diet can influence infant microbiome and a brilliant preprint highlighting the role women have played in science

General Microbiome

Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner. Lundgren SN. Microbiome.

Oral Microbiome

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease.Kazumichi Abe. PLos ONE

Gut Microbiome

Gut microbiota-immune-brain interactions in chemotherapy-associated behavioral comorbidities.Jordan KR Cancer

Analysis of the Gut Microbiome of Rural and Urban Healthy Indians Living in Sea Level and High Altitude Areas. Das B. Scientific Reports

Commentary:Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis.Agustí G. Frontier in Cellular and Infection Microbiology .

Animal Experiments and Microbiome

Non-nutritive sweeteners possess a bacteriostatic effect and alter gut microbiota in mice.Wang. PLoS One

The spleen microbiota of small wild mammals reveals distinct patterns with tick-borne bacteria. Ge Y. PLoS Neglected Tropical Diseases

Drosophila melanogaster establishes a species-specific mutualistic interaction with stable gut-colonizing bacteria.Pais IS. PLoS Biology

Plant, Soil, and Water Microbiome

Microbial community of tannery wastewater involved in nitrification revealed by Illumina MiSeq sequencing.Ma X. Journal of Microbiology and Biotechnology

Rhizosphere fungal community dynamics associated with Rehmannia glutinosa replant disease in a consecutive monoculture regime. Wu L Phytopathology.

Effects of soil erosion on agro-ecosystem services and soil functions: A multidisciplinary study in nineteen organically farmed European and Turkish vineyards. Costantini EAC. Journal of Environmental Management

Virome

Temporal dynamics of the lung and plasma viromes in lung transplant recipients Maia Segura-Wang. PLos ONE

Techniques

Mining Novel Constitutive Promoter Elements in Soil Metagenomic Libraries in <i>Escherichia coli</i>.Westmann CA. Frontier in Microbiology.

Taxonomic and Functional Compositions Impacted by the Quality of Metatranscriptomic Assemblies.Lau MCY. Frontiers in Microbiology.

Preprint

Illuminating women’s hidden contribution to the foundation of theoretical population genetics. Samantha Dung. bioRxiv

June 3, 2018

Today’s digest full of great and fun studies including a fungal survey of the atmosphere and links between gut microbiome and MS.

General Microbiome

RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions. Egert M. Methods

Environmental Sources of Bacteria Differentially Influence Host-Associated Microbial Dynamics.Cardona C. mSystems

Biohydrogen production from space crew’s waste simulants using thermophilic consolidated bioprocessing.Wang J. Bioresource Technology

Prevalence of <i>Trichomonas vaginalis</i> infection and protozoan load in South African women: a cross-sectional study.de Waaij DJ.BMJ Open

Time course metabolome of Roux-en-Y gastric bypass confirms correlation between leptin, body weight and the microbiome.Seridi L. PLoS One

Gut Microbiome

A gut feeling about multiple sclerosis.Quintana FJ. Proceedings of the National Academy of Sciences

Dietary fat and gut microbiota: mechanisms involved in obesity control.Coelho OGL. Critical Reviews in Food Science and Nutrition

Probiotic Species in the Modulation of Gut Microbiota: An Overview.Azad MAK J. Biomedical Research International.

The Relationship between Frequently Used Glucose-Lowering Agents and Gut Microbiota in Type 2 Diabetes Mellitus.Lv Y. Journal of Diabetes Research

The Gut Microbiome Profile in Obesity: A Systematic Review.Castaner O. International Journal of Endocrinology.

The <i>Lactobacillus</i> Bile Salt Hydrolase Repertoire Reveals Niche-Specific Adaptation.O’Flaherty S. mSphere

Skin Microbiome

Early-life skin microbiota in hospitalized preterm and full-term infants.Younge NE. Microbiome.

Oral Microbiome

Stimulated and unstimulated saliva samples have significantly different bacterial profiles.Gomar-Vercher S. PLoS

Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status.Presti RM. AIDS

Oral microbiota in youth with perinatally acquired HIV infection. Starr JR. Microbiome

Air and Water Microbiome

Biogeochemical probing of microbial communities in a basalt-hosted hot spring at Kverkfjöll volcano, Iceland.Cousins CR. Geobiology

Taxonomic diversity of fungi deposited from the atmosphere.Woo C. ISME Journal.

Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.Garcia SL. mSphere.

Animal Experiments and Microbiome

Thermal processing of food reduces gut microbiota diversity of the host and triggers adaptation of the microbiota: evidence from two vertebrates.Zhang Z. Microbiome

Longevity extension in Drosophila through gut-brain communication.Westfall S. Scientific Reports

Exploring the diversity-stability paradigm using sponge microbial communities.Glasl B. Scientific Reports

Exploring the Microbiome of Callinectes sapidus (Maryland Blue Crab).Ramachandran P. Genome Announcements

Effect of different types of olive oil pomace dietary supplementation on the rumen microbial community profile in Comisana ewes.Mannelli F. Scientific Reports

Variation in faecal microbiota in a group of horses managed at pasture over a 12-month period.Salem SE. Scientific Reports

Intestinal microbiota composition is altered according to nutritional biorhythms in the leopard coral grouper (Plectropomus leopardus).Mekuchi M. PLoS One

Characterization of the fecal and mucosa-associated microbiota in dogs with colorectal epithelial tumors.Herstad KMV.PLoS One

Fungal, Bacterial, and Archaeal Diversity in the Digestive Tract of Several Beetle Larvae (Coleoptera). Ziganshina EE. Biomedical Research International.

Plant and Soil Microbiomes

Antibiotic Resistance in Plant-Pathogenic Bacteria. Sundin GW. Annual Review of Phytopathology

Characterization of Microbial Communities in Pilot-Scale Constructed Wetlands with <i>Salicornia</i> for Treatment of Marine Aquaculture Effluents.Ma X. Archaea.

Fall Armyworm-Associated Gut Bacteria Modulate Plant Defense Responses.Acevedo FE. Molecular Plant-Microbe Interactions

Multifunctional potential of endophytic and rhizospheric microbial isolates associated with Butia purpurascens roots for promoting plant growth.da Silva CF. Antonie Van Leeuwenhoek

Rapid Microbial Community Changes During Initial Stages of Pine Litter Decomposition.Gołębiewski M. Microbial Ecology

In situ relationships between microbiota and potential pathobiota in Arabidopsis thaliana.Bartoli C. ISME Journal.

 

16 April, 2018

Today’s digest is packed with exciting research on links between gut microbiome and bone generation/development, also an interesting approach to fecal metabolome sampling

Gut Microbiome

Gut Microbiome and Bone.Ibáñez L. Joint Bone Spine

The protective effect of Lactobacillus and Bifidobacterium as the gut microbiota members against chronic urticaria.Rezazadeh A. International Immonopharmacology

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development.Pan WH. Genome Medicine

Fecal Microbiome

Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection.Seekatz AM. Anaerobe

Clostridium difficile stool shedding in infants hospitalized in two neonatal intensive care units is lower than previous point prevalence estimates using molecular diagnostic methods.Hines AG. BMC Pediatrics

 

Plant, Soil, and Water Microbiome

Metataxonomy and functionality of wood-tar degrading microbial consortia.Brusetti L. Journal of Hazardous Materials

In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments.Xie Y. Environmental Pollution

Biogas production and microbial community properties during anaerobic digestion of corn stover at different temperatures.Liu C. Bioresource Technology

Cadmium exposure and <i>Sedum alfredii</i> planting interactions shape the bacterial community in rhizosphere of the hyperaccumulator plant. Hou D. Applied Environmental Microbiology

Animal Experiments and Microbiome

The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria. Jung DH. Applied Microbiology and Biotechnology

Comparative biogeography of the gut microbiome between Jinhua and Landrace pigs.Xiao Y. Scientific Reports

Changes in the Rumen Epithelial Microbiota and Host Gene Expression of Cattle in Response to Alterations in Dietary Carbohydrate Composition.Petri RM. Applied Environmental Microbiology

Preprint

Mercury methylating microbial communities of boreal forest soils

Jingying Xu. bioRxiv

Techniques

Rat Fecal Metabolomics-Based Analysis.Deda O. Methods in Molecular Biology: Metabolic Profiling

Correction

Correction: <i>’Microbes in sport’ -The potential role of the gut microbiota in athlete health and performance</i>.British Journal of Sports Medicine

15 April, 2018

Today’s digest features an interesting article on microbial resevoirs in an urban setting, and influence of sequencing depth in chareterising the resistome .

General Microbiome

Diversity of the midstream urine microbiome in adults with chronic kidney disease.Kramer H. International Urology and Nephrology

Oral/Gut Microbiome

Quantitative Assessment of Shotgun Metagenomics and 16S rDNA Amplicon Sequencing in the Study of Human Gut Microbiome.Laudadio I. OMICS

The role of the gut microbiota in the pathology and prevention of liver disease.Altamirano-Barrera A. Journal of Nutritional Biochemistry

Effects of green tea on miRNA and microbiome of oral epithelium.Adami GR. Scientific Reports

Plant, Soils, and Water Microbiome

High-throughput sequencing reveals microbial communities in drinking water treatment sludge from six geographically distributed plants, including potentially toxic cyanobacteria and pathogens.Xu H. Science of Total Environment

Urban park soil microbiomes are a rich reservoir of natural product biosynthetic diversity.Charlop-Powers Z. PNAS

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience.Mandakovic D. Scientific Reports

Multivariate relationships between microbial communities and environmental variables during co-composting of sewage sludge and agricultural waste in the presence of PVP-AgNPs.Zhang L. Bioresources Technology

Animal Experiments and Microbiome

Gut microbiota recovery and immune response in ampicillin-treated mice.Castro-Mejía JL. Research in Veterinary Sciences

When the Nose Doesn’t Know: Canine Olfactory Function Associated With Health, Management, and Potential Links to Microbiota.Jenkins EK. Frontiers in Veterinary Sciences

Resistome

Microbiota transplantation and/or CRISPR-Cas in the battle against antimicrobial resistance.Vila J. Clinical Microbiology and Infection

Impact of sequencing depth on the characterization of the microbiome and resistome.Zaheer R. Scientific Reports

April 13, 2018

Today’s digest is short and sweet, but includes exciting science that explores how a vegan diet modulates the gut microbiome and new techniques for detection of DNA SNIPs.

General Microbiome

Effect of nisin on microbiome-brain-gut axis neurochemicals by Escherichia coli-induced diarrhea in mice.Jia Z. Microbial Pathogenesis

Food for Gut: Microbiota Fuels Immune Reconstitution after BMT.Simms-Waldrip TR. Cell Host and Microbe

 

Oral/Gut Microbiome

Small Intestine Microbiota Regulate Host Digestive and Absorptive Adaptive Responses to Dietary Lipids.Martinez-Guryn K. Cell Host and Microbe

Impact of a vegan diet on the human salivary microbiota. Hansen TH. Scientific Reports

 

Plant, Soils, and Water Microbiome

Bacterial communities of four adjacent fresh lakes at different trophic status. Ji B. Ecotoxicology and Environmental Safety

Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes.Wille L. Plant, Cell and Environment

Nitrogen enrichment suppresses other environmental drivers and homogenizes salt marsh leaf microbiome.Daleo P. Ecology

Different Recovery Processes of Soil Ammonia Oxidizers from Flooding Disturbance.Ye F. Microbial Ecology

d-Amino Acids Are Exuded by Arabidopsis thaliana Roots to the Rhizosphere.Hener C, Hummel S. International Journal of Molecular Sciences

 

Animal Microbiome and Experiments

Characterization of the ruminal fermentation and microbiome in lambs supplemented with hydrolysable and condensed tannins.Salami SA. FEMS Microbiology Ecology

Metagenomic discovery of novel enzymes and biosurfactants in a slaughterhouse biofilm microbial community.Thies S. Scientific Reports

Pasture Feeding Changes the Bovine Rumen and Milk Metabolome.O’Callaghan TF. Metabolites

Microbial metabolites, short-chain fatty acids, restrain tissue bacterial load, chronic inflammation, and associated cancer in the colon of mice.Kim M. European Journal of Immunology

Molecular diversity of the faecal microbiota of Toy Poodles in Japan.Omatsu T. Journal of Veterinary Medicine

Techniques

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments.Youngblut ND. Frontiers in Microbiology

February 4, 2018

Today’s digest is full of exciting papers and a great think piece on the questionable research practices.

General Microbiome

REVIEW:The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. Flandroy L. Science of The Total Environment

REVIEW: Designer microbiomes for environmental, energy and health biotechnology. Strous M. Current Opinion in Microbiology

Microbiome and atrial fibrillation. Mishima RS. International Journal of Cardiology

Gut Microbiome 

REVIEW:Role of gut microbiota and oxidative stress in the progression of non-alcoholic fatty liver disease to hepatocarcinoma: Current and innovative therapeutic approaches. Borrelli A. Redox Biology

Prebiotics/Probiotics

In vitro digestibility and prebiotic potential of curdlan (1 → 3)-β-d-glucan oligosaccharides in Lactobacillus species. Shi Y. Carbohydrate Polymers

No appendix necessary: Fecal transplants and antibiotics can resolve Clostridium difficile infection. Joshi T. Journal of Theoretical Biology.

Preprint

Evidence of independent acquisition and adaption of ultra-small bacteria to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria. McLean JS. bioRxiv

Ethical Shades of Gray: Questionable Research Practices in Health Professions Education. Artino AR. bioRxiv

Plant, Soil, and Water Microbiome

Biogeography and ecological processes affecting root-associated bacterial communities in soybean fields across China. Zhang B. Science of The Total Environment

Shift in the microbial community composition of surface water and sediment along an urban river. Wang L. Science of The Total Environment

REVIEW:Veterinary antibiotics (VAs) contamination as a global agro-ecological issue: A critical view. Kuppusamy S. Agriculture, Ecosystems & Environment

Rubber plantation ageing controls soil biodiversity after land conversion from cassava. Peerawat M. Agriculture, Ecosystems & Environment

Animal Experiment and Microbiome  

Gut microbiota modulates alcohol withdrawal-induced anxiety in mice. Xiao HW. Toxicology Letters

 Microbes in the News

Mosquitoes infected with bacteria to make them infertile released in battle against viruses.

-The Independent

Computer models reveal best way to kill deadly bacteria

        -Phys.Org

Bacteria produce gold by digesting toxic metals

-Phys.Org

SA start-up tackles deadly global bacteria

-SBS