June 13, 2018

A short Digest today with primarily preprints. A policy piece on diabetic patient care in the UK, Wolbachia strains never found before in Anopheles mosquitoes, and fecal pollution contributing to antibiotic resistant genes in waste water.

Jobs

Postdoctoral Fellowship in Microbiome Data Science – Johns Hopkins University

General microbiology

Preprint: DivIVA concentrates mycobacterial cell envelope assembly for initiation and stabilization of polar growth – Emily Sarah Melzer et al. – bioRxiv

Preprint: Genome-wide fitness assessment during diurnal growth reveals an expanded role of the cyanobacterial circadian clock protein KaiA – David G Welkie et al. – bioRxiv

Preprint: The fungal-specific Hda2 and Hda3 proteins regulate morphological switches in the human fungal pathogen Candida albicans – Misty Peterson et al. – bioRxiv

Preprint: Chance and pleiotropy dominate genetic diversity in complex bacterial environments – Lianet Noda-Garcia et al. – bioRxiv

Preprint: Molecular basis for the evolution of species-specific hemoglobin capture by pathogenic Staphylococcus – Jacob E Choby et al. – bioRxiv

Antibiotic resistance

Preprint: Comparison of trimethoprim-sulfamethoxazole versus ciprofloxacin monotherapy in Stenotrophomonas maltophilia bloodstream infections in children – Ahu Aksay et al. – bioRxiv

Preprint: The reduced prevalence of macrolide resistance in Mycoplasma pneumoniae clinical isolates from pediatric patients in Beijing in 2016 – Xiu jun Tian et al. – bioRxiv

Preprint: The key lethal effect existed in the antibacterial behavior of short, medium, and long chain fatty acid monoglycerides on Escherichia coli – Song Zhang et al. – bioRxiv

Human oral microbiome

Preprint: The stress hormone cortisol induces virulence in the oral microbiome – Ana Emilia Duran-Pinedo et al. – bioRxiv

Human gut microbiome

** Policy: Diabetes UK nutrition guidelines: reinforcing the foundations of diabetes care – Mark Greener – Practical Diabetes

Animal microbiome

** Preprint: Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa – Claire L Jeffries et al. – bioRxiv

Plant, root and soil microbiome

Preprint: The effect of susceptible and resistant potato cultivars on bacterial communities in the tuberosphere of potato in soil suppressive or conducive to common scab disease – Marketa Sagova-Mareckova et al. – bioRxiv

Preprint: Re-programming of Pseudomonas syringae pv. actinidiae gene expression during early stages of infection of kiwifruit – Peter McAtee et al. – bioRxiv

Water and extremophile microbiome

** Preprint: Fecal pollution explains antibiotic resistance gene abundances in anthropogenically impacted environments – Antti Karkman et al. – bioRxiv

Phages and viruses

Preprint: Adomaviruses: an emerging virus family provides insights into DNA virus evolution – Nicole L Welch et al. – bioRxiv

Preprint: Epstein-Barr Virus May Contribute to Central Nervous System Involvement in HIV-positive Individuals – Tommaso Lupia et al. – bioRxiv

Bioinformatics

Preprint: PorSignDB: a database of in vivo perturbation signatures for dissecting clinical outcome of PCV2 infection – Nicolaas Van Renne et al. – bioRxiv

June 3, 2018

Posted on June 3, 2018 by Itumeleng

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 Trichomonas vaginalis 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 Lactobacillus 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 Salicornia 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.

May 31, 2018

Posted on May 31, 2018 by anjacobson

Metagenomic analysis of the endangered kakapo fecal microbiota, a role for the microbiota in the social interaction habits of mice, using fecal metabolomics to readout functions of the gut microbiome.

General microbiome

Pre-print: Measuring the archaeome: detection and quantification of archaea signatures in the human body – Manuela R Pausan – bioRxiv

Human skin microbiome

Short‐term direct contact with soil and plant materials leads to an immediate increase in diversity of skin microbiota – Mira Grönroos – Microbiology Open

Human oral microbiome

Preliminary esophageal microbiome studies prompt important scientific questions – Yash Choksi – Clinical and Translational Gastroenterology

Human urinary microbiome

Calcium Oxalate Urolithiasis: A Case of Missing Microbes? – Carlos Alfredo Batagello – Journal of Endourology

Animal experiments

Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice – Roman M Stilling – eLIFE

Differences in cecal microbiome of selected high and low feather-pecking laying hens – P Birkl – Poultry Science

Digestive microbiota is different in pigs receiving antimicrobials or a feed additive during the nursery period – Cassandra Soler – PLOS ONE

Dietary supplementation with yeast hydrolysate in pregnancy influences colostrum yield and gut microbiota of sows and piglets after birth – Shah Hasah – PLOS ONE

Dietary sodium butyrate improves intestinal development and function by modulating the microbial community in broilers – Wei Wu – PLOS ONE

Animal microbiome

Network-guided genomic and metagenomic analysis of the faecal microbiota of the critically endangered kakapo – David W Waite – Scientific Reports

Bacterial diversity and community structure of the intestinal microbiome of Channel Catfish (Ictalurus punctatus) during ontogenesis – Francisca A Burgos – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Pre-print: Consortia of anti-nematode fungi and bacteria in the rhizosphere of soybean plants attacked by root-knot nematodes – Hirokazu Toju – bioRxiv

The importance of phyllosphere on plant functional ecology: a phyllo trait manifesto – Bruno H P Rosado – New Phytologist

Biocatalytic potential of Streptomyces spp. isolates from rhizosphere of plants and mycorrhizosphere of fungi – Jelena Spasic – Biotechnology and Applied Biochemistry

Hosts do not simply outsource pathogen resistance to protective symbionts – Jan Hrček – Evolution

Water and extremophile microbiome

Microbial Diversity in Sediments from the Bottom of the Challenger Deep, the Mariana Trench – Takuro Nunoura – Microbes and Environments

Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes – Amit Kumar – Microbial Ecology

Bloom of a denitrifying methanotroph, “Candidatus Methylomirabilis limnetica”, in a deep stratified lake – Jon S Graf – Environmental Microbiology

Food microbiology

Microbiome dynamics during spontaneous fermentations of sound grapes in comparison with sour rot and Botrytis infected grapes – Jessica Lleixà – International Journal of Food Microbiology

Pre-print: Microbial Community Structure and Diversity of Shrimp Paste at Different Fermentation Stages – Dai Lingying – bioRxiv

Bioinformatics

MetaHMM: A webserver for identifying novel genes with specified functions in metagenomic samples – Balázs Szalkai – Genomics

Metabolomics

The fecal metabolome as a functional readout of the gut microbiome – Jonas Zierer – Nature Genetics

More microbes

Pre-print: Aggregation of Vibrio cholerae by cationic polymers enhances quorum sensing but over-rides biofilm dissipation in response to autoinduction – Nicolas Perez-Soto – bioRxiv

Microbes in the news

Virus genes from city pond rescue bacteria – ScienceDaily

May 27, 2018

Posted on May 27, 2018 by Kiran

Pharmacobiomics, liver-microbiome axis, starvation effect on gut microbiota of shrimp, influence of gut microbiome on the larvae of a lepidopteran pest, microbiota of berries, building a local scientific community in data science and lots of articles for today’s digest.

General microbiome

Pharmacology in the age of the Holobiont – P Norvaisas – Current Opinion in Systems Biology

Dynamic bacterial and fungal microbiomes during sweet sorghum ensiling impact bioethanol production – D Gallagher – Bioresource Technology

Recovery of valuable metals from polymetallic mine tailings by natural microbial consortium – N Vardanyan – Environmental Technology

Variation in Electrode Redox Potential Selects for Different Microorganisms Under Cathodic Current Flow From Electrodes in Marine Sediments – BR Lam – Environmental Microbiology

Diurnal patterns of airborne algae in the Hawaiian Islands: a preliminary study – HW Singh – Aerobiologia

Novel human microbe-disease associations inference based on network consistency projection – S Zou – Scientific Reports

Multi-site human microbiome

Nitrate-responsive oral microbiome modulates nitric oxide homeostasis and blood pressure in humans – A Vanhatalo – Free Radical Biology and Medicine

Review: Biodiversity of the Human Oral Mycobiome in Health and Disease – HMHN Bandara – Oral Diseases

Human nearly-sterile sites

Human pegivirus persistence in the human blood virome after allogeneic haematopoietic stem cell transplantation – D-L Vu – Clinical Microbiology and Infection

Human gut microbiome

Review: Liver–Microbiome Axis in Health and Disease – TE Adolph – Trends in Immunology

Preprint: Crowdsourced study of children with autism and their typically developing siblings identifies differences in taxonomic and predicted function for stool-associated microbes using exact sequence variant analysis. – MM David – bioRxiv

Fecal and Mucosa-Associated Intestinal Microbiota in Patients with Diarrhea-Predominant Irritable Bowel Syndrome – N Maharshak – Digestive Diseases and Sciences

Prevention and treatment of Clostridium difficile associated diarrhea by reconstitution of the microbiota – N Eliakim-Raz – Human Vaccines & Immunotherapeutics

Animal experiments

Bifidobacterium spp. reshaping in the gut microbiota by low dose of juçara supplementation and hypothalamic insulin resistance in Wistar rats – G Jamar – Journal of Functional Foods

Salvianolic acid B alters the gut microbiota and mitigates colitis severity and associated inflammation – X Wu – Journal of Functional Foods

Metagenomics analysis of gut microbiota modulatory effect of green tea polyphenols by high fat diet-induced obesity mice model – X Zhang – Journal of Functional Foods

Starvation stress affects the interplay among shrimp gut microbiota, digestion and immune activities – W-F Dai – Fish & Shellfish Immunology

Helicobacter pylori-infected C57BL/6 mice with different gastrointestinal microbiota have contrasting gastric pathology, microbial and host immune responses – Z Ge – Scientific Reports

Animal microbiome

Preprint: The Gut-Associated Microbiome of the Eastern Spruce Budworm Does Not Influence Larval Growth or Survival – MT Schwarz – bioRxiv

Plant, root, and soil microbiome

Review: High content analysis of sea buckthorn, black chokeberry, red and white currants microbiota – A pilot study – J Lukša – Food Research International

Microbial functional responses to long-term anthropogenic impact in mangrove soils – L Cabral – Ecotoxicology and Environmental Safety

Foliage application of nitrogen has less influence on soil microbial biomass and community composition than soil application of nitrogen – X Huang – Journal of Soils and Sediments

Long-term and high-concentration heavy-metal contamination strongly influences the microbiome and functional genes in Yellow River sediments – Y Chen – Science of The Total Environment

Responses of atrazine degradation and native bacterial community in soil to Arthrobacter sp. strain HB-5 – J Gao – Ecotoxicology and Environmental Safety

Root bacterial endophytes confer drought resistance and enhance expression and activity of a vacuolar H+‐pumping pyrophosphatase in pepper plants – G Vigani – Environmental Microbiology

Defining plant growth promoting rhizobacteria molecular and biochemical networks in beneficial plant-microbe interactions – A Rosier – Plant and Soil

Roles of Plant-Associated Microbiota in Traditional Herbal Medicine – W Huang – Trends in Plant Science

Spatial structuring of soil microbial communities in commercial apple orchards – G Deakin – Applied Soil Ecology

Effects of root colonization by zinc-solubilizing bacteria on rice plant (Oryza sativa MR219) growth – NMI Othman – Agriculture and Natural Resources

Promising filamentous native fungi isolated from paddy soils for arsenic mitigation in rice grains cultivated under flooded conditions – FR Segura – Journal of Environmental Chemical Engineering

Soil respiration in Chinese tea gardens: autotrophic and heterotrophic respiration – LC Fan – European Journal of Soil Science

Water and extremophile microbiome

Methanonatronarchaeum thermophilum gen. nov., sp. nov. and ‘Candidatus Methanohalarchaeum thermophilum’, extremely halo(natrono)philic methyl-reducing methanogens from hypersaline lakes comprising a new euryarchaeal class Methanonatronarchaeia classis nov. – DY Sorokin – International Journal of Systematic and Evolutionary Microbiology

Food microbiology

The Genus Wallemia—From Contamination of Food to Health Threat – J Zajc- Microorganisms

Phages and viruses

Biological species in the viral world – L-M Bobay – PNAS

Genomic and ecological study of two distinctive freshwater bacteriophages infecting a Comamonadaceae bacterium – K Moon – Scientific Reports

Non-microbiology picks

Preprint: Building a local community of practice in scientific programming for Life Scientists – SLR Stevens – bioRxiv

May 24, 2018

Posted on May 24, 2018 by anjacobson

Pest gut microbiota indirectly effects plant defenses in corn, evolution of microbial social behavior from shearing in flow environments, a model to predict cytokine responses based on multi-comics data integration.

General microbiome

Shearing in flow environment promotes evolution of social behavior in microbial populations – Gurdip Uppal – eLIFE

Pregnancy and early life

Review: The Neonatal Microbiome and Its Partial Role in Mediating the Association between Birth by Cesarean Section and Adverse Pediatric Outcomes – D Montoya-Williams – Neonatology

Human respiratory microbiome

Chronic rhinosinusitis with nasal polyps is characterized by dysbacteriosis of the nasal microbiota – Thanit Chalermwatanachai – Scientific Reports

Human oral microbiome

Metagenomic study of bacterial microbiota in persistent endodontic infections using Next‐generation sequencing – G Sánchez-Sanhueza – International Endodontic Journal

Human gut microbiome

Iron Sequestration in Microbiota Biofilms As A Novel Strategy for Treating Inflammatory Bowel Disease – Jean-Paul Motta – Inflammatory Bowel Diseases

Temporal and long‐term gut microbiota variation in allergic disease: A prospective study from infancy to school age – Kotryna Simonyté Sjödin – European Journal of Allergy and Clinical Immunology

Bangladeshi children with acute diarrhea show fecal microbiomes with increased Streptococcus abundance, irrespective of diarrhea etiology – Silas Kieser – Environmental Microbiology

Animal experiments

Effects of a protease and essential oils on growth performance, blood cell profiles, nutrient retention, ileal microbiota, excreta gas emission, and breast meat quality in broiler chicks – J H Park – Poultry Science

Colonic Inhibition of Phosphatase and Tensin Homolog Increases Colitogenic Bacteria, Causing Development of Colitis in Il10-/- Mice – Jonathon Mitchell – Inflammatory Bowel Diseases

Review: Microbial Signatures as a Predictive Tool in IBD—Pearls and Pitfalls – Nadine Waldschmitt – Inflammatory Bowel Diseases

Oral hydroxysafflor yellow A reduces obesity in mice by modulating the gut microbiota and serum metabolism – Juan Liu – Pharmacological Research

Impact of commensal flora on periodontal immune response to lipopolysaccharide – Daiki Fukuhara – Journal of Periodontology

Animal microbiome

Poor feed efficiency in sheep is associated with several structural abnormalities in the community metabolic network of their ruminal microbes – Rocky D Patil – Journal of Animal Science

Plant, root, and soil microbiome

Cadmium phytoextraction potential of king grass (Pennisetum sinese Roxb.) and responses of rhizosphere bacterial communities to a cadmium pollution gradient – Li Hu – Environmental Science and Pollution Research

Gut-Associated Bacteria of Helicoverpa zea Indirectly Trigger Plant Defenses in Maize – Jie Wang – Journal of Chemical Ecology

Water and extremophile microbiome

Microbial activity during a coastal phytoplankton bloom on the Western Antarctic Peninsula in late summer – María E Alcamán-Arias – FEMS Microbiology Letters

Effects of partially saturated conditions on the metabolically active microbiome and on nitrogen removal in vertical subsurface flow constructed wetlands – Catiane Pelissari – Water Research

Pre-print: Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines – Andrian P Gajigan – PeerJ

Food microbiology

Porous Silicon-Based Biosensors: Towards Real-Time Optical Detection of Target Bacteria in the Food Industry – Naama Massad-Ivanir – Scientific Reports

Probiotics/prebiotics

Survival of Planktonic and Sessile Cells of Lactobacillus rhamnosus and Lactobacillus reuteri upon Exposure to Simulated Fasting-State Gastrointestinal Conditions – Kyle B Klopper – Probiotics and Antimicrobial Proteins

Phages and viruses

Pre-print: A novel oceanic uncultured temperate cyanophage lineage – José Flores-Uribe – bioRxiv

Bioinformatics

Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses – Olivier B Bakker – Nature Immunology

More microbes

Pre-print: New sequential touch method for determining bacterial contact transfer rate from finger to surface – Pengcheng Zhao – bioRxiv

Amy’s non-microbiology picks

Restoration of paper artworks with microemulsions confined in hydrogels for safe and efficient removal of adhesive tapes – Nicole Bonelli – PNAS

May 23, 2018

Posted on May 23, 2018 by edwardmessick

Today’s digest is packed full of awesome gut microbiome studies, a bunch of plant/soil studies, new features to QIIME and other bioinformatics, as well as a good serving of interesting pre-prints, editorials, and doctoral theses. Enjoy!

General microbiome

Microbial micropatches within microbial hotspots – Lisa M. Dann – PLOS ONE

Pregnancy and early life

The matter of the reproductive microbiome – Sam Schoenmakers – Obstetric Medicine

* Gestational diabetes is associated with change in the gut microbiota composition in third trimester of pregnancy and postpartum – Mie Korslund Wiinblad Crusell – Microbiome

The importance of appropriate initial bacterial colonization of the intestine in newborn, child, and adult health – W Allan Walker – Pediatric Research

Human oral microbiome

Oral health status in historic population: Macroscopic and metagenomic evidence – Claire Willmann – PLOS ONE

The Subgingival Microbiome of Periodontal Pockets With Different Probing Depths in Chronic and Aggressive Periodontitis: A Pilot Study – Meng Shi – Frontiers in Cellular and Infection Microbiology

Human gut microbiome

[Pre-print] Gut microbiota markers in obese adolescent and adult patients: age-dependent differential patterns – Federica Del Chierico – Frontiers in Microbiology

Clinical applications of gut microbiota in cancer biology – Sunny H. Wong – Seminars in Cancer Biology

* Microbiome-Mediated Effects of the Mediterranean Diet on Inflammation – Melisa A Bailey – Advances in Nutrition

** Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury – Benjamin M Howard – Trauma Surgery & Acute Care Open

* Hypoxia induces senescence of bone marrow mesenchymal stem cells via altered gut microbiota – Junyue Xing – Nature Communications

Animal experiments

The bacterial and archaeal community structures and methanogenic potential of the cecal microbiota of goats fed with hay and high-grain diets – Wei Jin – Antonie van Leeuwenhoek

Effects of whole-grain rice and wheat on composition of gut microbiota and short-chain fatty acids in rats – Fei Han – Journal of Agriculture and Food Chemistry

Animal microbiome

Diet breadth and exploitation of exotic plants shift the core microbiome of Cephaloleia, a group of tropical herbivorous beetles – Chelsea L. Blankenchip – PeerJ

Altered gut microbiota associated with intestinal disease in grass carp (Ctenopharyngodon idellus) – Ngoc Tuan Tran – World Journal of Microbiology and Biotechnology

The gut microbiome is associated with behavioural task in honey bees – J. C. Jones – Insectes Sociaux

The role of the gut microbiome in health and disease of adult honey bee workers – Kasie Raymann – Current Opinion in Insect Science

Plant, root, and soil microbiome

Microbial communities in soil profile are more responsive to legacy effects of wheat-cover crop rotations than tillage systems – Anil Somenahally – Soil Biology and Biochemistry

New insights into the effects of support matrix on the removal of organic micro-pollutants and the microbial community in constructed wetlands – Liang Zhang – Environmental Pollution

[Doctoral thesis] Imprint of management on microbial communities in arable soil – Putz, Martina

Study of microbial diversity in plant–microbe interaction system with oil sludge contamination – Dhote, Monika – International Journal of Phytoremediation

Effect of different potassium levels on nitrogen metabolism, nitrogen bacteria and nitrogen archaea bacteria communities in rhizosphere of tobacco plant – WENG Zebin – Acta Tabacaria Sinica

Canola Root–Associated Microbiomes in the Canadian Prairies – Chih-Ying Lay – Frontiers in Microbiology

Leaf-associated bacterial microbiota of coffee and its correlation with manganese and calcium levels on leaves – Leandro Pio de Sousa – Genetics and Molecular Biology

[Review] Organic Amendments, Beneficial Microbes, and Soil Microbiota: Toward a Unified Framework for Disease Suppression – Giuliano Bonanomi – Annual Review of Phytopathology

[Pre-print] Metagenomic sequencing provides insights into the location of microbial detoxification in the gut of a small mammalian herbivore – Kevin D. Kohl – bioRxiv

[Pre-print] Archaeal, bacterial, and eukaryal microbial community structure of sediment and seawater in a coastal region near Puerto Nuevo, Baja California – Sabah Ul-Hasan – bioRxiv

Water and extremophile microbiome

Deterministic mechanisms define the long-term anaerobic digestion microbiome and its functionality regardless of the initial microbial community – M.Peces – Water Research

Built environment

[Editorial] Microbiome Yarns: microbiome of the built environment, paranormal microbiology, and the power of single cell genomics – Kenneth Timmis – microbial biotechnology

New Techniques for the Generation and Analysis of Tailored Microbial Systems on Surfaces – Ariel L. Furst – Biochemistry

* [Pre-print] Strainlevel overlap between infant and hospital fungal microbiomes revealed through de novo assembly of eukaryotic genomes from metagenomes – Matthew R. Olm – bioRxiv

Probiotics / prebiotics

The effects of probiotics supplementation on metabolic health in pregnant women: An evidence based meta-analysis – Jia Zheng – PLOS ONE

Bioinformatics

[Pre-print / doctoral thesis] Recovering 2,032 Baltic Sea microbial genomes by optimized metagenomic binning – Alneberg, Johannes – DiVA

** Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin – Nicholas A. Bokulich – Microbiome

Techniques

Functional Genomics Approaches to Studying Symbioses between Legumes and Nitrogen-Fixing Rhizobia – Martina Lardi – High-Throughput

VSITA, an Improved Approach of Target Amplification in the Identification of Viral Pathogens – Yi Zhang – Europe PMC

Making and Sequencing Heavily Multiplexed, High-Throughput 16S Ribosomal RNA Gene Amplicon Libraries Using a Flexible, Two-Stage PCR Protocol – Ankur Naqib – Gene Expression Analysis

Ed’s non-microbiology picks

The Environmental Protection Agency in the Early Trump Administration: Prelude to Regulatory Capture

Perspectives on the Great Amazon Reef: Extension, Biodiversity, and Threats

Fasting boosts stem cells’ regenerative capacity

Eggs not linked to cardiovascular risk, despite conflicting advice

Noninvasive spinal stimulation method enables paralyzed people to regain use of hands, study finds

Cannabidiol significantly reduces seizures in patients with severe form of epilepsy

May 21, 2018

Posted on May 21, 2018 by aalexiev

A long update to make up for the past few days, with extra emphasis on Plant/root/soil studies and water studies!

General microbiome

Why do microbes exhibit weak biogeographic patterns? – Kyle M. Meyer, ISME

Understanding and designing the strategies for the microbe-mediated remediation of environmental contaminants using omics approaches – Muneer A. Malla, Frontiers in Microbiology

Two-year microbial adaptation during hydrogen-mediated biogas upgrading process in a serial reactor configuration – L. Treu, Bioresource Technology

Microbial ecology

Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi – Alberto Amato, ISME

Cooperation, competition and antibiotic resistance in bacterial colonies – Isabel Frost, ISME

Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchlorate-reducing communities – Tyler P. Barnum, ISME

Diversity and Hidden Host Specificity of Chytrids infecting Colonial Volvocacean Algae – Silke Van den Wyngaert, Journal of Eukaryotic Microbiology

Human bone microbiome

Understanding the microbiome of diabetic foot osteomyelitis: insights from molecular and microscopic approaches – Khalid Johani, Clinical Microbiology and Infection

Human oral microbiome

Bacterial-derived exopolysaccharides enhance antifungal drug tolerance in a cross-kingdom oral biofilm – Dongyeop Kim, ISME

Human vaginal microbiome

Metabolomics as a clinical testing method for the diagnosis of vaginal dysbiosis – Emiley Watson, American Journal of Reproductive Immunology

Human gut microbiome

Design and rationale of the INSYTE study: A randomised, placebo controlled study to test the efficacy of a synbiotic on liver fat, disease biomarkers and intestinal microbiota in non-alcoholic fatty liver disease – Eleonora Scorletti, Contemporary Clinical Trials

Gastrointestinal Disorders Associated with Primary Immunodeficiency Diseases – Stella Hartono, Clinical Reviews in Allergy & Immunology

Impact on the quality of life of an episode of Clostridium difficileinfection in a hospital setting – A. Duburcq, Journal of Epidemiology and Public Health

Animal experiments

Inhalational exposure to particulate matter air pollution alters the composition of the gut microbiome – Ece A. Mutlu, Environmental Pollution

Effects of long-term intake of a yogurt fermented with Lactobacillus delbrueckii subsp.bulgaricus 2038 and Streptococcus thermophilus1131 on mice – Yuki Usui, International Immunology

Dietary mung bean protein reduces high-fat diet-induced weight gain by modulating host bile acid metabolism in a gut microbiota-dependent manner – Akiho Nakatani, Biochemical and Biophysical Research Communications

Dietary nitrate modulates gut microbiota profile and prevents the activation of mucosal inflammatory pathways induced by broad-spectrum antibiotics – Bárbara S. Rocha, Free Radical Biology and Medicine

Animal microbiome

Coral bleaching from a single cell perspective – Daniel Aagren Nielsen, ISME

Plant, root, and soil microbiome

Lack of thinning effects over inter-annual changes in soil fungal community and diversity in a Mediterranean pine forest – Carles Castaño, Forest Ecology and Management

Response of soil microbial communities to agroecological versus conventional systems of extensive agriculture – Diego N. Chavarria, Agriculture, Ecosystems & Environment

Intraspecific variation in indirect plant–soil feedbacks influences a wetland plant invasion – Warwick J. Allen, Ecology

Native bacteria promote plant growth under drought stress condition without impacting the rhizomicrobiome – Elisabeth Armada, FEMS Microbiology Ecology

Plant roots redesign the rhizosphere to alter the three‐dimensional physical architecture and water dynamics – Sheikh M. F. Rabbi, New Phytologist

The Invasive Brazilian Pepper Tree (Schinus terebinthifolius) Is Colonized by a Root Microbiome Enriched With Alphaproteobacteria and Unclassified Spartobacteria – Karim Dawkins, Frontiers in Microbiology

Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation – Marie-Francoise Noirot-Gros, Frontiers in Microbiology

The Emergence of Endophytic Microbes and Their Biological Promise – Gary Strobel, Journal of Fungi

Changes in soil nitrogen dynamics caused by prescribed fires in dense gorse lands in SW Pyrenees – Leire Múgica, Science of The Total Environment

Response of soil microbial communities to agroecological versus conventional systems of extensive agriculture – Diego N. Chavarria, Agriculture, Ecosystems & Environment

Application of biosolids drives the diversity of antibiotic resistance genes in soil and lettuce at harvest – Lu Yang, Soil Biology and Biochemistry

Mycorrhizal Status In Endemic Pipewort: Eriocaulon eurypeplon Körn (Fam: Eriocaulaceae) – Vishal R. Kamble, IOSR Journal of Pharmacy and Biological Sciences

Model formulation of microbial CO2production and efficiency can significantly influence short and long term soil C projections – Ford Ballantyne IV & Sharon A. Billings, ISME

Effect of endophytic fungus Piriformospora indica on yield and some physiological traits of millet (Panicum miliaceum) under water stress – Goudarz Ahmadvand, Crop and Pasture Science

Composition and functional genes analysis of bacterial communities from urban parks of Shanghai, China and their role in ecosystem functionality – Xin Wang, Landscape and Urban Planning

Plant, fungal, bacterial, and nitrogen interactions in the litter layer of a native Patagonian forest – Lucía Vivanco, PeerJ

Root-exuded coumarin shapes the root microbiome – Derek S. Lundberg, PNAS

Deforestation decreases spatial turnover and alters the network interactions in soil bacterial communities – Jing Tian, Soil Biology and Biochemistry

Distinct nitrogen provisioning from organic amendments in soil as influenced by farming system and water regime – Martina Lori, Frontiers in Microbiology

Biodiversity of urban soils for sustainable cities – C. Guilland, Environmental Chemistry Letters

Predator–prey mass ratio drives microbial activity under dry conditions in Sphagnum peatlands – Monika K. Reczuga, Ecology and Evolution

Organic and Biofertilization on Crop Production in Semiarid Regions – Ayman M. Helmy, The Handbook of Environmental Chemistry

Prevalence of Botrytis cinerea at different phenological stages of table grapes grown in the northern region of South Africa – Patricia C. Carmichael, Scientia Horticulturae

Water and extremophile microbiome

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast – Cene Gostinčar, BMC Genomics

Interactive effects of multiple stressors revealed by sequencing total (DNA) and active (RNA) components of experimental sediment microbial communities – Simone C. Birrer, Science of The Total Environment

Physicochemical drivers of microbial community structure in sediments of Lake Hazen, Nunavut, Canada – Matti O. Ruuskanen, Frontiers in Microbiology

Strains of the toxic and bloom-forming Nodularia spumigena (cyanobacteria) can degrade methylphosphonate and release methane – Jonna E. Teikari, ISME

Seasonal resource conditions favor a summertime increase in North Pacific diatom–diazotroph associations – Christopher L. Follett, ISME

Predator and prey biodiversity relationship and its consequences on marine ecosystem functioning—interplay between nanoflagellates and bacterioplankton – Jinny Wu Yang, ISME

Light and temperature control the seasonal distribution of thaumarchaeota in the South Atlantic bight – Qian Liu, ISME

Distributions of phytoplankton carbohydrate, protein and lipid in the world oceans from satellite ocean colour – Shovonlal Roy, ISME

Relationship between dissolved organic matter quality and microbial community composition across polar glacial environments – H J Smith, FEMS Microbiology Ecology

Sediment depth-dependent spatial variations of bacterial communities in mud deposits of the eastern China marginal seas – Yanlu Qiao, Frontiers in Microbiology

Food microbiology

Origin and varietal based proteomic and peptidomic fingerprinting of Theobroma cacao in non-fermented and fermented cocoa beans – Neha Kumari, Food Research International

Metagenomic and metatranscriptomic analysis of the microbial community in Swiss-type Maasdam cheese during ripening – Ilhan Cem Duru, International Journal of Food Microbiology

Combined effect of cold atmospheric plasma, intrinsic and extrinsic factors on the microbial behavior in/on (food) model systems during storage – C. Smet, Innovative Food Science & Emerging Technologies

Polyphenols from selected dietary spices and medicinal herbs differentially affect common food-borne pathogenic bacteria and lactic acid bacteria – Chak-Lun Chan, Food Control

Probiotics

Enhanced viability of probiotics (Pediococcus pentosaceusLi05) by encapsulation in microgels doped with inorganic nanoparticles – Mingfei Yao, Food Hydrocolloids

Dysbiosis of microbiome and probiotic treatment in a genetic model of autism spectrum disorders – Tabouy Laure, Brain, Behavior, and Immunity

Bioinformatics

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation – Han Zhang, Nucleic Acids Research

A Multi-Omics Database for Parasitic Nematodes and Trematodes – John Martin, Eukaryotic Genomic Databases

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis – Jasmine Chong, Nucleic Acids Research

AAI-profiler: fast proteome-wide exploratory analysis reveals taxonomic identity, misclassification and contamination – Alan J Medlar, Nucleic Acids Research

Techniques

Mutant phenotypes for thousands of bacterial genes of unknown function – Morgan N. Price, Nature

Methods for Generating Microbial Cocultures that Grow in the Absence of Fixed Carbon or Nitrogen – Matthew J. Smith, Synthetic Biology

Development of a 16S rRNA-targeted fluorescence in situ hybridization probe for quantification of the ammonia-oxidizer Nitrosotalea devanaterra and its relatives – C.X. Restrepo-Ortiz, Systematic and Applied Microbiology

Creation of a fibre categories database to quantify different dietary fibres – Stacey Fuller, Journal of Food Composition and Analysis

May 16, 2018

Posted on May 16, 2018 by JP Cardenas

Today we have a interesting set of reviews. In addtion: research about virome in infants, microbiome changes in Alzheimer’s disease and changes in neonate and maternal microbiome under gestational diabetes. We have also the report of the Oral Microbiome Bank of China and some papers about invertebrate microbiome.

Human/General Microbiome

Review: Microbiome-Immune Interactions and Liver Disease – James H. Tabibian – Clinical Liver Disease

Review: Microbial Metabolism in the Mammalian Gut: Molecular Mechanisms and Clinical Implications – Anne Hall – Journal of Pediatric Gastroenterology and Nutrition

Review: Starch Tolerance and the Short Bowel – Jan de Laffolie – Journal of Pediatric Gastroenterology and Nutrition

Review: Microbial Fermentation of Starch: Its Impact on the Range of Acceptable Carbohydrate Intake – Satish C. Kalhan – Journal of Pediatric Gastroenterology and Nutrition

Review: Pathways and mechanisms linking dietary components to cardiometabolic disease: thinking beyond calories – K. L. Stanhope – Obesity Reviews

Review: On the potential role of intestinal microbial community in hepatocarcinogenesis in chronic hepatitis B – Ashraf Mohamadkhani – Cancer Medicine

Review: The gut microbiota and the brain-gut-kidney axis in hypertension and chronic kidney disease – Tao Yang – Nature Reviews Nephrology

Review: Epithelial Barrier Dysfunctions in Atopic Dermatitis: A Skin-Gut-Lung Model Linking Microbiome Alteration and Immune Dysregulation – T.H. Zhu – British Journal of Dermatology

Review: Association between Fusobacterium nucleatum and colorectal cancer: Progress and future directions – Sheng Zhang – Journal of Cancer

Viromes of one year old infants reveal the impact of birth mode on microbiome diversity – Angela McCann – PeerJ

Dysbiosis of maternal and neonatal microbiota associated with gestational diabetes mellitus – Jinfeng Wang – Gut

Analysis of Gut Microbiome and Diet Modification in Patients with Crohn’s Disease – Sumathi Sankaran Walters – SOJ Microbiology & Infectious Diseases

Gut Microbiome is Altered in Patients with Alzheimer’s Disease – Zhuang, Zhen-Qian – Journal of Alzheimer’s Disease

The Oral Microbiome Bank of China – Peng Xian – International Journal of Oral Science

Animal Microbiome

Microbiota modification by probiotic supplementation reduces colitis associated colon cancer in mice – Maria Carolina S Mendes – World Journal of Gastroenterology

A cytokine network involving IL-36γ, IL-23, and IL-22 promotes antimicrobial defense and recovery from intestinal barrier damage – Vu L. Ngo – PNAS

Biodegradation of polyethylene and plastic mixtures in mealworms (larvae of Tenebrio molitor) and effects on the gut microbiome – Anja Malawi Brandon – Environmental Science and Technology

Supplementation with organic acids showing different effects on growth performance, gut morphology and microbiota of weaned pigs fed with highly or less digestible diets – S. Li – Journal of Animal Science

Metagenomics Analysis of Gut Microbiota in a High Fat Diet-Induced Obesity Mouse Model Fed with (-)-Epigallocatechin 3-O-(3-O-Methyl) Gallate (EGCG3”Me) – Xin Zhang – Molecular Nutrition and Food Research

Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing – Francisca Zepeda-Paulo – PeerJ

Uncovering the hidden players in Lepidoptera biology: the heritable microbial endosymbionts – Anne Duplouy – PeerJ

The influence of diet and environment on the gut microbial community of field crickets – Soon Hwee Ng – Ecology and Evolution

Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii – Wenya Zhang – Ecology and Evolution

Food Microbiome

The changes of dominant lactic acid bacteria and their metabolites during corn stover ensiling – Zhenshang Xu – Journal of Applied Microbiology

Characterization of the Microbiota in Air- or Vacuum-Packed Crisp Grass Carp ( Ctenopharyngodon idella C. et V.) Fillets by 16S rRNA PCR-Denaturing Gradient Gel Electrophoresis and High-Throughput Sequencing – Ziqiang Pan – Journal of Food Protection

Succession of bacterial microbiota in tilapia fillets at 4 °C and in situ investigation of spoilers – Shan Duan – World Journal of Microbiology and Biotechnology

Bioinformatics/Genomics

Preprint: Measures of reproducibility in sampling and laboratory processing methods in high-throughput microbiome analysis – Patricia Vera-Wolf (and featuring our Microbiome Digest founder, Elisabeth Bik) – BioRxiv

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments – Alexandre Almeida – GigaScience

Uncovering the drivers of host-associated microbiota with joint species distribution modeling – Johannes R. Björk – Molecular Ecology

Beneficial Microbes and Compounds

Review: Vitamin D in inflammatory bowel disease: more than just a supplement – John Gubatan – Current Opinion in Gastroenterology

Review: Bleach for Atopic Dermatitis – Melody Maarouf – Dermatitis

Simultaneous Amelioratation of Colitis and Liver Injury in Mice by Bifidobacterium longum LC67 and Lactobacillus plantarum LC27 – Se-Eun Jang – Scientific Reports

Pathogens

Cross-specificity of protective human antibodies against Klebsiella pneumoniae LPS O-antigen – Tim Rollenske – Nature Immunology

Environmental Microbiome (including Built environments)

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study – Julia K.Nuy – Science of The Total Environment

Fine grained compositional analysis of Port Everglades Inlet microbiome using high throughput DNA sequencing – Lauren O’Connell – PeerJ

Antimicrobial Resistance

Emerging Infectious Diseases, Antimicrobial Resistance and Millennium Development Goals: Resolving the Challenges through One Health – G. V. Asokan – Central Asian Journal of Global Health

Other

Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins – Nitzan Koppel – eLife

The Interaction of Anti-diabetic α-Glucosidase Inhibitors and Gut Bacteria α-Glucosidase – Kemin Tan – Protein Science

	Francis W on The Hetch Hetchy Railroad
	Best Practice Exchan… on June 1, 2018
	May 17, 2024 \| Micro… on May 15, 2024
	Kathy Brown on The Hetch Hetchy Railroad
	John Wilbur on The Hetch Hetchy Railroad

Microbiome Digest – Bik's Picks

A daily digest of scientific microbiome papers, by the MD team. Founded by Elisabeth Bik, microbiome and science integrity consultant. Twitter: @microbiomdigest

Category Archives: Human oral

June 13, 2018

June 12, 2018

June 8, 2018

June 3, 2018

May 31, 2018

May 27, 2018

May 24, 2018

May 23, 2018

May 21, 2018

May 16, 2018