June 13, 2018

Today’s microbiology highlights: Microbiome in pregnancies, microbiome of SLE, Mycobacteria of a karst region, skin microbiome of non-human mammals. And lab diversity, potential problem in big data, Paris climate agreement of 1.5⁰C increase among the non-microbe highlights.

General microbiome

Biochemical, molecular and antibiotic resistance profile of multi-potential toluene metabolizing bacteria isolated from tannery effluents – F Muccee – bioRxiv

Pregnancy and early life

Review: Microbiome in normal and pathological pregnancies: A literature overview – CR Taddei – AJRI

Multi-site human microbiome

Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells – AP Chan – Scientific Reports

Human gut microbiome

Proton Pump Inhibitor Initiation and Withdrawal affects Gut Microbiota and Readmission Risk in Cirrhosis – JS Bajaj – AJG

Review: Early-Life Food Nutrition, Microbiota Maturation and Immune Development Shape Life-Long Health – X Zhou – Critical Reviews in Food Science and Nutrition

Animal experiments

Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota – F Cignarella – Cell Metabolism

The Microbiome and Systemic Lupus Erythematosus – JT Rosenbaum – The New England Journal of Medicine

Review: The probiotic effectiveness in experimental colitis is correlated with gut microbiome and host genetic features – S Suwal – bioRxiv

Animal microbiome

Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia – AA Ross – PNAS

Alterations in the gut (Gallus gallus) microbiota following the consumption of zinc biofortified wheat (Triticum aestivum) -based diet – S Reed – ACS

Water and extremophile microbiome

Nontuberculous mycobacteria in the environment of Hranice Abyss, the world’s deepest flooded cave (Hranice karst, Czech Republic) – I Pavlik – Environmental Science and Pollution Research

Built environment

Toxicity assessment of pharmaceutical compounds on mixed culture from activated sludge using respirometric technique: The role of microbial community structure – IA Vasiliadou – Science of The Total Environment

Food microbiology

Effect of herbal feed additives on performance parameters, intestinal microbiota, intestinal morphology and meat lipid oxidation of broiler chickens – I Giannenas – British Poultry Science

Techniques

Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research – PD Schloss – mBio

Next-Generation Sequencing Could be a Promising Diagnostic Approach for Pathogen Detection: Pathogenic Analysis of Pediatric Bacterial Meningitis by Next-Generation Sequencing Technology Directly from Cerebrospinal Fluid Specimens – L Guo – bioRxiv

Microbes in the news

Media Advisory: Live exhibit of dance and song on tiny world of bacteria inside us comes to Buffalo Museum of Science – UB News Center

Non-microbiology picks

These labs are remarkably diverse — here’s why they’re winning at science – Nature

Big data little help in megafauna mysteries – Nature

What does it take to make an institution more diverse? – Nature

The many possible climates from the Paris Agreement’s aim of 1.5 °C warming – Nature

June 5, 2018

Posted on June 5, 2018 by anjacobson

A model to study the effect of horizontal gene transfer on maintaining equilibrium in microbial communities, antimicrobial tolerance in brewery biofilms, the sperm whale microbiota.

General microbiome

Horizontal Gene Transfer Can Help Maintain the Equilibrium of Microbial Communities – Yuhang Fan – Journal of Theoretical Biology

Human gut microbiome

Review: Carcinogenesis as a Result of Multiple Inflammatory and Oxidative Hits: a Comprehensive Review from Tumor Microenvironment to Gut Microbiota – Floriana Morgillo – Neoplasia

Animal experiments

Extrathymically Generated Regulatory T Cells Establish a Niche for Intestinal Border-Dwelling Bacteria and Affect Physiologic Metabolite Balance – Clarissa Campbell – Immunity

Animal microbiome

Pre-print: Microbiome interaction networks and community structure from lab-reared and field-collected Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus mosquito vectors – Shivanand Hegde – bioRxiv

Pre-print: Metagenomics reveals diet-specific specialization in fungus gardens of grass- and dicot-cutter ants – Lily Khadempour – bioRxiv

Occurrence of anthropozoonotic parasitic infections and faecal microbes in free-ranging sperm whales (Physeter macrocephalus) from the Mediterranean Sea – Carlos Hermosilla – Parasitology Research

Plant, root, and soil microbiome

Root-associated bacteria influencing mycelial growth of Tricholoma matsutake (pine mushroom) – Seung-Yoon Oh – Journal of Microbiology

Determinants of Soil Bacterial and Fungal Community Composition Toward Carbon-Use Efficiency Across Primary and Secondary Forests in a Costa Rican Conservation Area – Katie M McGee – Microbial Ecology

Water and extremophile microbiome

Pre-print: Competition and Synergy Between Prochlorococcus and Synechococcus Under Ocean Acidification Conditions – James Jeffrey Morris – bioRxiv

Quantifying the Relative Contributions of Environmental Sources to the Microbial Community in an Urban Stream under Dry and Wet Weather Conditions – Darshan Baral – Applied and Environmental Microbiology

The deep continental subsurface: the dark biosphere – Cristina Escudero – International Microbiology

Food microbiology

Competitive inter-species interactions underlie the increased antimicrobial tolerance in multispecies brewery biofilms – Ilse Parijs – ISME Journal

Phages and viruses

Influence of gut microbiome on mucosal immune activation and SHIV viral transmission in naive macaques – Yongjun Sui – Mucosal Immunity

Techniques

Does universal 16S rRNA gene amplicon sequencing of environmental communities provide an accurate description of nitrifying guilds? – Vaibhav Diwan – Journal of Microbiological Methods

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 29, 2018

Posted on May 29, 2018 by TinaS

Today we have an interesting review discussing the best practices for performing a microbiome study by R. Knight, “Microbial wars” – a brief overview on microbial competition by M.A. Bauer. Check many other interesting papers, particularly “crowded” section of Soil microbes, while in news you can read how scientists tested bacteria’s power to boost broccoli growth in space. Enjoy!

General microbiome

Review: Best practices for analysing microbiomes – Rob Knight – Nature Reviews Microbiology

Microbial wars: Competition in ecological niches and within the microbiome – Maria A. Bauer – Microbial Cell

Review: Concepts and Methods to Access Novel Antibiotics from Actinomycetes – Joachim J. Hug – Antibiotics

Human gut microbiome

Gut Microbiota and Human Health: Insights From Ecological Restoration – Matthew R. Orr – The Quarterly Review of Biology

Maternal omega-3 fatty acids regulate offspring obesity through persistent modulation of gut microbiota – Ruairi C. Robertson – Microbiome

Current Evidence for the Management of Inflammatory Bowel Diseases Using Fecal Microbiota Transplantation – Seong Ran Jeon – Current Infectious Disease Reports

The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species – Melhem Bilen – Microbiome

Animal experiments

Gut microbes contribute to variation in solid organ transplant outcomes in mice – Christine M. McIntosh – Microbiome

Animal microbiome

Necessary Sequencing Depth and Clustering Method to Obtain Relatively Stable Diversity Patterns in Studying Fish Gut Microbiota – Fanshu Xiao – Current Microbiology

Microbial shifts in the swine nasal microbiota in response to parenteral antimicrobial administration – Mohamed Zeineldin – Microbial Pathogenesis

Photobacterium malacitanum sp. nov., and Photobacterium andalusiense sp. nov., two new bacteria isolated from diseased farmed fish in Southern Spain – Alejandro M. Labella – Systematic and Applied Microbiology

Plant, root, and soil microbiome

Effects of genetically modified Burkholderia pyrrocinia JK-SH007E1 on soil microbial community in poplar rhizosphere – L. He – Forest Pathology

Dynamics of soil nitrogen fractions and their relationship with soil microbial communities in two forest species of northern China – Dong Liu – PLOS One

Short-term transcriptional response of microbial communities to N-fertilization in a pine forest soil – Michaeline B.N. Albright – Applied and Environmental Microbiology

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

Dynamics of soil nitrogen fractions and their relationship with soil microbial communities in two forest species of northern China – Dong Liu – PLOS One

Effects of winter snowpack and nitrogen addition on the soil microbial community in a temperate forest in northeastern China – Guoyong Yan – Ecological Indicators

Responses of soil bacterial communities to Conyza canadensis invasion with different cover classes along a climatic gradient* – Congyan Wang – CLEAN Soil Water

Shifts in microbial community structure and soil nitrogen mineralization following short-term soil amendment with the ammonifier Bacillus amyloliquefaciens DT – Cai Hui – International Biodeterioration & Biodegradation

Restoration with pioneer plants changes soil properties and remodels the diversity and structure of bacterial communities in rhizosphere and bulk soil of copper mine tailings in Jiangxi Province, China – Xiaoyan Sun – Environmental Science and Pollution Research

Enhancer assisted-phytoremediation of mercury-contaminated soils by Oxalis corniculata L., and rhizosphere microorganism distribution of Oxalis corniculata L. – Zhongchuang Liu – Ecotoxicology and Environmental Safety

Draft Genome Sequence of the Plant Growth-Promoting Sphingobium sp. Strain AEW4, Isolated from the Rhizosphere of the Beachgrass Ammophila breviligulata – Abanoub E. Wanees – Genome Announcements

Cultivar-specific response of bacterial community to cadmium contamination in the rhizosphere of rice (Oryza sativa L.) – Dandi Hou – Environmental Pollution

Elevated CO2 increases the abundance but simplifies networks of soybean rhizosphere fungal community in Mollisol soils – Zhenhua Yu – Agriculture, Ecosystems & Environment

Suppression of Alternaria blight disease and plant growth promotion of mustard (Brassica juncea L.) by antagonistic rhizosphere bacteria – R. Sharma – Applied Soil Ecology

Water and extremophile microbiome

Salipaludibacillus halalkaliphilus sp. nov., a moderately haloalkaliphilic bacterium from a coastal-marine wetland – Mohammad Ali Amoozegar – International Journal of Systematic and Evolutionary Microbiology

Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia – Amjad B. Khalil – BioMed Research International

Seasonal dynamics of bacterioplankton community in a large, shallow, highly dynamic freshwater lake – Zhaoyu Kong – Canadian Journal of Microbiology

Sediment microbial communities influenced by cool hydrothermal fluid migration – Laura A. Zinke – Frontiers in Microbiology / Extreme Microbiology

Microbial interactions with dissolved organic matter drive carbon dynamics and community succession’ – Xiaoqin Wu – Frontiers in Microbiology / Microbiological Chemistry and Geomicrobiology

Metabolites change of Scenedesmus obliquus exerted by AgNPs – Pu Wang – Journal of Environmental Sciences

Built environment

Cultivable microbial diversity associated with cellular phones – Rashmi Kurli – Frontiers in Microbiology / Systems Microbiology

Food microbiology

A bioinformatics pipeline integrating predictive metagenomics profiling for the analysis of 16S rDNA/rRNA sequencing data originated from foods – Marios Mataragas – Food Microbiology

Phages and viruses

Identification of a bacteriophage from an environmental multidrug-resistant E. coli isolate and its function in horizontal transfer of ARGs – Qiang Wang – Science of The Total Environment

Metagenomic analysis of the RNA fraction of the fecal virome indicates high diversity in pigs infected by porcine endemic diarrhea virus in the United States – Qi Chen – Virology Journal

Bioinformatics

Evaluating the use of diversity indices to distinguish between microbial communities with different traits – Sergey Feranchuka – Research in Microbiology

Taxonomic and functional compositions impacted by the quality of metatranscriptomic assemblies – Maggie Lau – Frontiers in Microbiology – Microbiological Chemistry and Geomicrobiology

Biotechnology

Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples – Zhichao Zhou – Applied Microbiology and Biotechnology

Systems analysis of phosphate-limitation-induced lipid accumulation by the oleaginous yeast Rhodosporidium toruloides – Yanan Wang – Biotechnology for Biofuels

Review: A decade of understanding secondary metabolism in Pseudomonas spp. for sustainable agriculture and pharmaceutical applications – Izzah Shahid – Environmental Sustainability

Microbes in the news

Could we work together with our bacteria to stop infection?

Scientists test bacteria’s power to boost broccoli growth in space

May 28, 2018

Posted on May 28, 2018 by Kiran

In our short digest today, you could read articles on animal experiments and pre-prints on techniques!

Human gut microbiome

Preprint: Using molecular ecological network analysis to explore the effects of chemotherapy on intestinal microbial communities of colorectal cancer patients – J Cong – bioRxiv

Animal experiments

Anti-diabetic effect of baicalein is associated with the modulation of gut microbiota in streptozotocin and high-fat-diet induced diabetic rats – B Zhang – Journal of Functional Foods

Effects of limestone inclusion on growth performance, intestinal microbiota, and the jejunal transcriptomic profile when fed to weaning pigs – L Blavi – Animal Feed Science and Technology

Plant, root, and soil microbiome

Soil microbiological attributes indicate recovery of an iron mining area and of the biological quality of adjacent phytophysiognomies – AO Silva – Ecological Indicators

Water and extremophile microbiome

Response of microbial populations regulating nutrient biogeochemical cycles to oiling of coastal saltmarshes from the Deepwater Horizon oil spill – H-S Bae – Environmental Pollution

Techniques

Preprint: Using the Wax moth larva Galleria mellonella infection model to detect emerging bacterial pathogens – R Hernandez – bioRxiv

Preprint: Isolation and antibiotic profile of Vibrio spp. final effluents of two wastewater treatment plants in the Eastern Cape of South Africa – O Osuolale – bioRxiv

Conventional wastewater treatment and reuse site practices modify bacterial community structure but do not eliminate some opportunistic pathogens in reclaimed water – P Kulkarni – Science of The Total Environment

Effect of temperature and pH on the community dynamics of coagulase-negative staphylococci during spontaneous meat fermentation in a model system – DA Stavropoulou – Food Microbiology

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 26, 2018

Posted on May 26, 2018 by aalexiev

We have a big variety of topics covered in today’s posts, from built environment to bat microbiome to biolfilms!

Biofilms

Genomic identification of microbial species adhering to maxillofacial prostheses and susceptibility to different hygiene protocols – Juliana Barchelli, The Journal of Bioadhesion and Biofilm Research

Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses – Wei Ding, The Journal of Bioadhesion and Biofilm Research

Microbial ecology

Keystone taxa as drivers of microbiome structure and functioning – Samiran Banerjee, Nature Reviews Microbiology

Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems – Akshit Goya, Physical Review Letters

Pregnancy and early life

Iron supplementation has minor effects on gut microbiota composition in overweight and obese women in early pregnancy – Marloes Dekker Nitert, British Journal of Nutrition

Human respiratory microbiome

The concordance between upper and lower respiratory microbiota in children with Mycoplasma pneumoniae pneumonia – Wenkui Dai, Emerging Microbes & Infections

The lung microbiome in children with HIV-bronchiectasis: a cross-sectional pilot study – Refiloe Masekela, BMC Pulmonary Medicine

Human skin microbiome

Does Lindioil (Indirubin) treatment affect the composition of Malassezia species on psoriatic skin? – Y. K. Lin, British Journal of Dermatology

Shift in skin microbiota of Western European women across aging – Romain Jugé, Journal of Applied Microbiology

Human vaginal microbiome

Understanding mucosal and microbial functionality of the female reproductive tract by metaproteomics: Implications for HIV transmission – Alicia R. Berard, American Journal of Reproductive Immunology

Vaginal microbiome studies in pregnancy must also analyse host factors – S.S. Witkin, BJOG: An International Journal of Obstetrics & Gynaecology

Vaginal microbiome in early pregnancy and subsequent risk of spontaneous preterm birth: a case‐control study – Negar Tabatabaei, BJOG: An International Journal of Obstetrics & Gynaecology

Human gut microbiome

Structural Alteration of Gut Microbiota during the Amelioration of Human Type 2 Diabetes with Hyperlipidemia by Metformin and a Traditional Chinese Herbal Formula: a Multicenter, Randomized, Open Label Clinical Trial – Xiaolin Tong, mBio

The role of diet in the aetiopathogenesis of inflammatory bowel disease – Hamed Khalili, Nature Reviews Gastroenterology & Hepatology

Animal experiments

Ethanolamine enhances intestinal functions by altering gut microbiome and mucosal anti-stress capacity in weaned rats – Jian Zhou, British Journal of Nutrition

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

Evaluation of the impact of glyphosate and its residues in feed on animal health – European Food Safety Authority (EFSA), EFSA Journal

Risks for animal health related to the presence of fumonisins, their modified forms and hidden forms in feed – EFSA Panel on Contaminants in the Food Chain (CONTAM), EFSA Journal

Plateau hypoxia attenuates the metabolic activity of intestinal flora to enhance the bioavailability of nifedipine – Juanhong Zhang, Drug Delivery

Animal microbiome

Fecal Microbiota Composition Changes after a Body Weight Loss Diet in Beagle Dogs – A Salas, Journal of Animal Sciences

The fecal bacterial microbiota of bats; Slovenia – Modest Vengust, PLOS One

Plant, root, and soil microbiome

Fertilization shapes a well-organized community of bacterial decomposers for accelerated paddy straw degradation – Yushan Zhan, Scientific Reports

Paddy-upland rotation for sustainable agriculture with regards to diverse soil microbial community – Ping-Fu Hou, Scientific Reports

Annual post‐market environmental monitoring report on the cultivation of genetically modified maize MON 810 in 2016 – European Food Safety Authority (EFSA), EFSA Journal

Conserved Responses in a War of Small Molecules between a Plant-Pathogenic Bacterium and Fungi – Joseph E. Spraker, mBio

Pseudomonads contribute to regulation of Pratylenchus penetrans (Nematoda) populations on apple – Tristan T. Watson, Canadian Journal of Microbiology

Water and extremophile microbiome

Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm – Jennifer M. Michaud, Nature Communications

Combined genotyping, microbial diversity and metabolite profiling studies on farmed Mytilus spp. from Kiel Fjord – Caroline Utermann, Scientific Reports

Bathyarchaeota: globally distributed metabolic generalists in anoxic environments – Zhichao Zhou, FEMS Microbiology Reviews

Probiotics / prebiotics

Dietary fibers, prebiotics, and exopolysaccharides produced by lactic acid bacteria: potential health benefits with special regard to cholesterol-lowering effects – E. Korcz, Food and Function

Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies – Concetta Panebianco, Microbiome

Built environment

City-scale distribution and dispersal routes of mycobiome in residences – Xinzhao Tong, Microbiome

Unraveling bacterial fingerprints of city subways from microbiome 16S gene profiles – Alejandro R. Walker, Biology Direct

Bioinformatics

ASaiM: a Galaxy-based framework to analyze microbiota data – Bérénice Batut, GigaScience

Comprehensive benchmarking and ensemble approaches for metagenomic classifiers – Alexa B. R. McIntyre, Genome Biology

Techniques

The Present and Future of Whole Genome Sequencing (WGS) and Whole Metagenome Sequencing (WMS) for Surveillance of Antimicrobial Resistant Microorganisms and Antimicrobial Resistance Genes across the Food Chain – Elena A. Oniciuc, Genes

A microbial endocrinology-based simulated small intestinal medium for the evaluation of neurochemical production by gut microbiota – Daniel N Villageliú, FEMS Microbiology Ecology

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

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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: Extremophiles

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