19 September, 2018

Today’s midweek digest includes a brilliant review on the occurrence of HGT within human holobiont and a new approach to analysing microbiome data

General Microbiome

REVIEW: Prokaryotic horizontal gene transfer within the human holobiont: ecological-evolutionary inferences, implications and possibilities.Sitaraman R. Microbiome

Epidemiological aspects of healthcare-associated infections and microbial genomics.Mirande C. Europeans Journal of Clinical Microbiology and Infectious Diseases

Association between Cigarette Smoking Status and Composition of Gut Microbiota: Population-Based Cross-Sectional Study. Lee SH. Journal of Clinical Medicine

REVIEW: Proteomics and the microbiome: pitfalls and potential.Lin H. Expert Review of Proteomics

Biological films adhering to the oral soft tissues: structure, composition and potential impact on taste perception.Neyraud E. Journal of Texture Studies

Restriction enzyme digestion of host DNA enhances universal detection of parasitic pathogens in blood via targeted amplicon deep sequencing. Flaherty BR. Microbiome

Single-cell genomics of co-sorted Nanoarchaeota suggests novel putative host associations and diversification of proteins involved in symbiosis.Jarett JK. Microbiome

The Extended Genotype: Microbially Mediated Olfactory Communication.Carthey AJR. Trends in Ecology and Evolution

Ceftriaxone administration disrupts intestinal homeostasis, mediating non-inflammatory proliferation and dissemination of commensal enterococci.Chakraborty R. Infection and Immunity

Gut Microbiome

Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly.Martínez I. eLIFE

Human gut <i>Bacteroides</i> capture vitamin B<sub>12</sub> via cell surface-exposed lipoproteins.Wexler AG. eLIFE

Structural basis for the role of serine-rich repeat proteins from <i>Lactobacillus reuteri</i> in gut microbe-host interactions.Sequeira S. PNAS

Rapid and complete dehalogenation of halonitromethanes in simulated gastrointestinal tract and its influence on toxicity. Yin J. Chemosphere.

Diet: Cause or Consequence of the Microbial Profile of Cholelithiasis Disease?Gutiérrez-Díaz I. Nutrients

Immobilization stress-induced Escherichia coli causes anxiety by inducing NF-κB activation through gut microbiota disturbance. Jang HM. Scientific Reports

Salmonella stimulates pro-inflammatory signalling through p21-activated kinases bypassing innate immune receptors.Sun H. Nature Microbiology

Lung Microbiome

Deciphering the Lung Microbiome: Implications for Lung Health and Disease.Johnson MM. Respiration

Plant and Soil Microbiome

Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico. Sánchez-Soto Jiménez MF. PeerJ.

Insight into Bacterial Community Diversity and Monthly Fluctuations of Medicago sativa Rhizosphere Soil in Response to Hydrogen Gas Using Illumina High-Throughput Sequencing. Li Z. Current Microbiology

Molecular characterization and detection of 16SrIII group phytoplasma associated with Huanglongbing symptoms.Wulff NAA. Phytopathology

Water Microbiome

Analysis of Bacterial Community Structure of Activated Sludge from Wastewater Treatment Plants in Winter. Xu S. BioMed Research International

Biological As(III) oxidation in biofilters by using native groundwater microorganisms.Crognale S. Science of the Total Environment

Animal Experiments and Microbiome

Lignocellulose degradation at the holobiont level: teamwork in a keystone soil invertebrate. Bredon M. Microbiome

The impact of chemerin or chemokine-like receptor 1 loss on the mouse gut microbiome.Dranse HJ. PeerJ

Techniques

KERNEL-PENALIZED REGRESSION FOR ANALYSIS OF MICROBIOME DATA.Randolph TW. The Annals of Applied Statistics

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12 September​​ 2018

Today’s digest is full of exciting microbiome reviews and new techniques for analysing microbiome datasets.

General Microbiome

Complete genome sequence of Bifidobacterium choerinum FMB-1, a resistant starch-degrading bacterium.Jung DH. Journal of Biotechnology

Gut Microbiome

REVIEW: Nutritional Modulation of Innate Immunity: The Fat-Bile-Gut Connection.Chevre R. Trends in Endocrinology and Metabolism

Plant, Soil, and Water Microbiome

Microbial composition, potential functional roles and genetic novelty in gypsum-rich and hypersaline soils of Monegros and Gallocanta (Spain). Menéndez-Serra M.Science of the Total Environment

Combined polyhydroxyalkanoates (PHA) and 1,3-propanediol production from crude glycerol: Selective conversion of volatile fatty acids into PHA by mixed microbial consortia.Burniol-Figols A. Water Research

Quantification of Agrobacterium vitis from Grapevine Nursery Stock and Vineyard Soil using Droplet Digital PCR.Voegel TM. Plant Disease

Below-ground-above-ground Plant-microbial Interactions: Focusing on Soybean, Rhizobacteria and Mycorrhizal Fungi. Igiehon NO. The Open Microbiology Journal

Animal Experiments and Microbiome

Effects of exogenous microbial inoculum on the structure and dynamics of bacterial communities in swine carcass composting. Yang X. Canadian Journal of Microbiology

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing.Couper L. Journal of Visualized Experiments

Effects of dietary lysozyme levels on growth performance, intestinal morphology, immunity response and microbiota community of growing pigs. Zou L. Journal of the Science of Food and Agriculture

REVIEW: A Review of the Effect of Management Practices on <i>Campylobacter</i> Prevalence in Poultry Farms.Sibanda N. Frontiers in Microbiology.

Metabolic Syndrome During Perinatal Period in Sows and the Link With Gut Microbiota and Metabolites. Cheng C. Frontiers in Microbiology

Fecal Microbiota Transplantation Ameliorates Experimentally Induced Colitis in Mice by Upregulating AhR. Wei YL. Frontiers in Microbiology

Prebiotics and Probiotics

Probiotic <i>Lactobacillus plantarum</i> Promotes Intestinal Barrier Function by Strengthening the Epithelium and Modulating Gut Microbiota. Wang J. Frontiers in Microbiology

Uterine Microbiome

Commentary: Uterine Microbiota: Residents, Tourists, or Invaders?Altmäe S. Frontier in Immunology.

Technique

Preservation of microbial DNA in marine sediments: Insights from extracellular DNA pools. Torti A. Environmental Microbiology

REVIEW: Hypothesis Testing and Statistical Analysis of Microbiome. Xia Y. Genes and Diseases

A Zero-inflated Beta-binomial Model for Microbiome Data Analysis.Hu T. Stat

August 13, 2018

Today’s Digest is full of amazing research from focusing on causation in microbiome studies to increased efficacy of BLAST searches in the age of high throughput sequencing.

General Microbiome

Microbiome: Focus on Causation and Mechanism.Fischbach MA. Cell.

Effect of Antibiotic-Mediated Microbiome Modulation on Rotavirus Vaccine Immunogenicity: A Human, Randomized-Control Proof-of-Concept Trial.Harris VC. Cell Host and Microbe

Enhancing Rotavirus Vaccination: A Microbial Fix? Parker EPK. Cell Host and Microbe

Snapshot of an early Paleoproterozoic ecosystem: Two diverse microfossil communities from the Turee Creek Group, Western Australia. Barlow EV. Geobiology.

Background levels of microorganisms in the busy urban environment of transport hubs.Patel KV. Journal of Applied Microbiology.

Immunomodulation as Therapy for Fungal Infection: Are We Closer?Sam QH. Frontiers in Microbiology

Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA.Grahl N. mSphere.

Oral Microbiome

Comparison of oral microbiota in orthodontic patients and healthy individuals.Sun F. Microbial Pathogenesis

Skin Microbiome

Mud therapy and skin microbiome: a review.Antonelli M. International Journal of Biometeorology

Gut Microbiome

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.Bradley PH. PLoS Computational Biology

Dynamic changes in human-gut microbiome in relation to a placebo-controlled anthelminthic trial in Indonesia.Martin I. PLoS Neglected Tropical Disease.

Faecal Microbiome

Effects of metal and metalloid pollutants on the microbiota composition of feces obtained from twelve commercial pig farms across China.Peng Z. Science Total Environment

Fecal Microbiota Alterations Associated With Diarrhea-Predominant Irritable Bowel Syndrome.Zhuang X. Frontiers in Microbiology.

Plant, Soils, and Air Microbiome

Environmental variables better explain changes in potential nitrification and denitrification activities than microbial properties in fertilized forest soils.Tang Y. Science of Total Environment

Metagenomic analysis of rhizosphere microflora of oil-contaminated soil planted with barley and alfalfa. Kumar V. PLoS One.

Trichoderma polysporum selectively inhibits white-nose syndrome fungal pathogen Pseudogymnoascus destructans amidst soil microbes.Singh A. Microbiome.

Tissue Microbiome of Norway Spruce Affected by Heterobasidion-Induced Wood Decay.Ren F. Microbial Ecology

Evidence for complete nitrification in enrichment culture of tidal sediments and diversity analysis of clade a comammox Nitrospira in natural environments. Yu C. Applied Microbiology and Biotechnology.

Traits-Based Integration of Multi-Species Inoculants Facilitates Shifts of Indigenous Soil Bacterial Community.Wang J. Frontier in Microbiology

Spatial Patterns and Drivers of Microbial Taxa in a Karst Broadleaf Forest.Song M. Frontiers in Microbiology

Water Microbiome

Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.Berner C. Frontiers in Microbiology

Coral Microbiome Database: Integration of sequences reveals high diversity and relatedness of coral-associated microbes.Huggett MJ. Environmental Microbiology Reports

Animal Experiments and Microbiome

Diet and other environmental factors shape the bacterial communities of fish gut in an eutrophic lake. Kashinskaya EN. Journal of Applied Microbiology

Yeast-like microorganisms in the scale insect Kermes quercus (Insecta, Hemiptera, Coccomorpha: Kermesidae). Newly acquired symbionts?Podsiadło E. Arthropod Structure and Development

Initial description of the core ocular surface microbiome in dogs: Bacterial community diversity and composition in a defined canine population.Leis ML. Veterinary Ophthalmology

High-Throughput Analysis Reveals Seasonal Variation of the Gut Microbiota Composition Within Forest Musk Deer (<i>Moschus berezovskii</i>).Hu X. Frontiers in Microbiology

A Comprehensive Research on Antibiotic Resistance Genes in Microbiota of Aquatic Animals.Hong B. Frontiers in Microbiology

Identification of spider-mite species and their endosymbionts using multiplex PCR.Zélé F. Experimental and Applied Acarology

Soil microarthropods alter the outcome of plant-soil feedback experiments.Kuťáková E. Scientific Reports

Techniques/Bioinformatics 

Metagenome complexity and template length are the main causes of bias in PCR-based bacteria community analysis.Peng W. Journal of Basic Microbiology

Single-cell RNA sequencing technologies and bioinformatics pipelines.Hwang B. Experimental and Molecular Medicine

Negative Binomial Mixed Models for Analyzing Longitudinal Microbiome Data.Zhang X. Frontiers in Microbiology

Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems. Hu Y. Scientific Reports

CrocoBLAST: Running BLAST efficiently in the age of next-generation sequencing.Tristão Ramos RJ. Bioinformatics

23 July, 2018

Today’s digest includes exciting Microbiome events and brilliant papers on animal microbiomes. Lastly, research exploring the war on gluten.

Events

Microbiome X Regulation 1 Panel discussion on navigating the FDA

Introduction to the 4th International Symposium on Gluten-Free Cereal Products and Beverages.

General Microbiome

Antibiotic Scars Left on the Gut Microbiota from the Stringent Response. Yi H. Trends in Microbiology

Genomic inference of the metabolism and evolution of the archaeal phylum Aigarchaeota. Hua ZS. Nature Communications

Genomic Characterization of Sulphite Reducing Bacteria Isolated From the Dairy Production Chain.Doyle CJ. Frontiers in Microbiology.

How Microbial Aggregates Protect against Nanoparticle Toxicity.Tang J. Trends in Biotechnology.

Inhibition of microbial spoilage of grass carp (Ctenopharyngodon idellus) fillets with a chitosan-based coating during refrigerated storage. Yu D. International Journal of Food Microbiology

Gut Microbiome

The gut microbiome and irritable bowel syndrome. Menees S. F1000Research

Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism.Zarrinpar A. Nature Communications

Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease. Zhang X. Nature Communications

Techniques

A rapid PCR-based method to discriminate Macrococcus caseolyticus and Macrococcus canis from closely-related Staphylococcus species based on the ctaC gene sequence. Mazhar S. Journal of Microbiological Methods

MetaVW: Large-Scale Machine Learning for Metagenomics Sequence Classification. Vervier K. Methods in Molecular Biology

Soil, Water, and Air Microbiome

Influence of new agromining cropping systems on soil bacterial diversity and the physico-chemical characteristics of an ultramafic soil. Saad RF. Science of the Total Environment

<i>Pseudomonas chlororaphis</i> produces multiple R-tailocin particles that broaden the killing spectrum and contribute to persistence in rhizosphere communities.Dorosky RJ. Applied and Environmental Microbiology

REVIEW: Microbial diversity and biogeography in Arctic soils.Malard LA. Environmental Microbiology Reports.

Impact of brine and antiscalants on reef-building corals in the Gulf of Aqaba – Potential effects from desalination plants.Petersen KL. Water Research

Mapping the Bacterial Community in Digboi Oil Refinery, India by High-Throughput Sequencing Approach. Dasgupta A.  Current Microbiology.

Chemical-, site-, and taxa-dependent benthic community health in coastal areas of the Bohai Sea and northern Yellow Sea: A sediment quality triad approach. Khim JS. Science of the Total Environment.

Animal Experiments and Microbiome

Microbial Biogeography Along the Gastrointestinal Tract of a Red Panda. Zeng Y. Frontiers in Microbiology

REVIEW:The gut microbiota of wild rodents: Challenges and opportunities. Viney M. Laboratory Animals

Genome-wide association studies of inflammatory bowel disease in German shepherd dogs. Peiravan A. PLoS One.

Effects of Rodent Diet Choice and Fiber Type on Data Interpretation of Gut Microbiome and Metabolic Disease Research.Pellizzon MA. Current Protocols in Toxicology

Non-Microbiology Hot Pick

The war on gluten. Servick K. Science.

 

 

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

 

 

 

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.