June 14, 2018

Microbial inhabitants of chimpanzee beds, the California cat flea microbiome, butterfly-associated bacterial communities.

General microbiome

Bistability in a system of two species interacting through mutualism as well as competition: Chemostat vs. Lotka-Volterra equations – Stefan Vet – PLOS ONE

Multi-site human microbiome

Review: The interaction between iNKT cells and the mucosal microbiota – Fatma Zehra Hapil – Immunology

Human skin microbiome

Cutibacterium acnes (Propionibacterium acnes) and acne vulgaris: a brief look at the latest updates – B Dréno – Journal of the European Academy of Dermatology and Venereology

Human gut microbiome

Review: Gut dysbiosis: a potential link between increased cancer risk in ageing and inflammaging – Arya Biragyn – The Lancet Oncology

The microbiome of translocated bacterial populations in patients with and without inflammatory bowel disease – Christopher John Kiely – Internal Medicine Journal

Animal experiments

Oxaliplatin-induced changes in microbiota, TLR4+ cells and enhanced HMGB1 expression in the murine colon – Vanesa Stojanovska – PLOS ONE

Bifidobacteria attenuate the development of metabolic disorders, with inter- and intra-species differences – Guangsu Zhu – Food & Function

Immunomodulation and effects on microbiota after in ovo administration of chicken cathelicidin-2 – Tryntsje Cuperus – PLOS ONE

Animal microbiome

Apparent Total Tract Macronutrient Digestibility, Serum Chemistry, Urinalysis, and Fecal Characteristics, Metabolites and Microbiota of Adult Dogs Fed Extruded, Mildly Cooked, and Raw Diets – Kiley M Algya – Journal of Animal Science

Assessing Cat Flea Microbiomes in Northern and Southern California by 16S rRNA Next-Generation Sequencing – Elton J R Vasconcelos – Vector-Bronze and Zoonotic Diseases

Pre-print: High similarity in the microbiota of cold-water sponges of the Genus Mycale from two different geographical areas – César A Cárdenas – PeerJ

Synchronized shift of oral, faecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction – Muriel Dietrich – Royal Society Open Science

Dietary and developmental shifts in butterfly-associated bacterial communities – Kruttika Phalnikar – Royal Society Open Science

Plant, root, and soil microbiome

Impact of pyrometallurgical slags on sunflower growth, metal accumulation and rhizosphere microbial communities – A C Agnello – Chemosphere

Direct and indirect effects of a pH gradient bring insights into the mechanisms driving prokaryotic community structures – Daniel R Lammel – Microbiome

Review: A three-act play: pentachlorophenol threats to the cork oak forest soils mycobiome – Adélia Varela – Current Opinion in Microbiology

Soil homogenization and microedges: perspectives on soil‐based drivers of plant diversity and ecosystem processes – Holly J Stover – Ecosphere

Soils beneath different arctic shrubs have contrasting responses to a natural gradient in temperature – Qiong Zhao – Ecosphere

Effects of straw return on bacterial communities in a wheat-maize rotation system in the North China Plain – Dali Yu – PLOS ONE

Pre-print: Convergent gain and loss of genomic islands drives lifestyle changes in plant-associated bacteria – Ryan A Melnyk – bioRxiv

Water and extremophile microbiome

Vertical and horizontal biogeographic patterns and major factors affecting bacterial communities in the open South China Sea – Yi Li – Scientific Reports

Built environment

Ecology of sleeping: the microbial and arthropod associates of chimpanzee beds – Megan S Thoemmes – Royal Society Open Science

Bacteria art

Creative Culture: Bacterial Art Project Combines Art and Science – Candice Dyer – Brenau Window Online

Science, career, and publishing

Bioinformatics core competencies for undergraduate life sciences education – Melissa A Wilson Sayres – PLOS ONE

Pre-print: Outcomes of early NIH-funded investigators: Experience of the National Institute of Allergy and Infectious Diseases – Patricia A Haggerty – bioRxiv

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June 13, 2018

Events and jobs

Computational scientists (from post-master to postdoc fellowships) in metagenomics and microbial genomics : Trento, Italy – The Laboratory of Computational Metagenomics

General microbiome

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative – Jun Wang, Microbiome Announcement

Microbial ecology

Everything is not everywhere: a tale on the biogeography of cyanobacteria – Karine Felix Ribeiro, Hydrobiologia

A Meta‐Analysis of Temperature Sensitivity as a Microbial Trait – Charlotte J. Alster, Global Change Biology

Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities – John Davison, ISME

Bacillus thuringiensis produces the lipopeptide thumolycin to antagonize microbes and nematodes – Dehong Zheng, Microbiological Research

Qualitative analysis of biosurfactants from Bacillus species exhibiting antifungal activity – Ambrin Sarwar, Plos One

Antarctic cryptoendolithic fungal communities are highly adapted and dominated by Lecanoromycetes and Dothideomycetes – Claudia Coleine, Frontiers in Microbiology

Pregnancy and early life

The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis – Stephen Wandro, mSphere

The role of breast milk in the colonization of neonatal gut and skin with coagulase-negative staphylococci – Hiie Soeorg, Pediatric Research

Multisite human microbiome

Prion-like Propagation of α-synuclein in the gut-brain axis – Ying Chen, Brain Research Bulletin

Microbiome-Gut-Brain Axis and Toll-Like Receptors in Parkinson’s Disease – Valentina Caputi, International Journal of Molecular Sciences

Current Insights in Microbiome Shifts in Sjogren’s Syndrome and Possible Therapeutic Interventions – Christina Tsigalou, Frontiers in Immunology

Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome between Neonatal Intensive Care Unit (NICU) Environments – Suchitra K. Hourigan, Frontiers in Microbiology

Human skin microbiome

Skin Microbiota in Obese Women at Risk for Surgical Site Infection After Cesarean Delivery – Kara M. Rood, Scientific Reports

Cutibacterium acnes (Propionibacterium acnes) and acne vulgaris: a brief look at the latest updates – B. Dréno, Journal of the European Academy of Dermatology and Venereology

Characterisation of Cutibacterium acnes phylotypes in acne and in vivo exploratory evaluation of Myrtacine® – S. Pécastaings, Journal of the European Academy of Dermatology and Venereology

Human oral microbiome

Analysis of the oral microbiome on the surface of modified dental polymers – Denise  Tornavoi de Castro, Archives of Oral Biology

Genetic Association with Subgingival Bacterial Colonization in Chronic Periodontitis – Franco Cavalla, Genes

Biological and cultural drivers of oral microbiota in Medieval and Post-Medieval London, UK – Andrew G Farrer, bioRxiv

Human gut microbiome

Breath methane concentrations and markers of obesity in patients with functional gastrointestinal disorders – Clive H. Wilder-Smith, United European Gastroenterology Journal

The Intersection Between Colonization Resistance, Antimicrobial Stewardship, and Clostridium difficile – Rossana Rosa, Current Infectious Disease Reports

Celiac Disease and Fecal Microbiota Transplantation: A New Beginning? – Shmuel Golfeyz MD, Correspondence

Gut microbiota metabolites, amino acid metabolites and improvements in insulin sensitivity and glucose metabolism: the POUNDS Lost trial – Yoriko Heianza, Nutrition

Cutting the Gordian Knot of the Microbiota – Kimberly S.Vasquez, Molecular Cell

Host: Microbiome co-metabolic processing of dietary polyphenols – An acute, single blinded, cross-over study with different doses of apple polyphenols in healthy subjects – Kajetan Trost, Food Research International

Clinical trials of kimchi intakes on the regulation of metabolic parameters and colon health in healthy Korean young adults – Hee-Young Kim, Journal of Functional Foods

Animal experiments

Propolis from Different Geographic Origins Suppress Intestinal Inflammation in a Model of DSS‐Induced Colitis is Associated with Decreased Bacteroides spp. in the Gut – Kai Wang, Molecular Nutrition and Food Research

Effect of direct-fed microbials on culturable gut microbiotas in broiler chickens: a meta-analysis of controlled trials – Chhaiden Heak, Asian-Australasian Journal of Animal Sciences

A dietary isothiocyanate-enriched moringa (Moringa oleifera) seed extract improves glucose tolerance in a high-fat-diet mouse model and modulates the gut microbiome – Asha Jaja-Chimedza, Journal of Functional Foods

The enteric microbiota regulates jejunal Paneth cell number and function without impacting intestinal stem cells – Alexi A. Schoenborn, Gut Microbes

Comprehensive longitudinal microbiome analysis of the chicken cecum reveals a shift from competitive to environmental drivers and a window of opportunity for Campylobacter – Umer Zeeshan Ijaz, bioRxiv

Microbial quantity impacts Drosophila nutrition, development, and lifespan – Erin S. Keebaugh, iScience

Absence of Gut Microbiota Reduces Emotional Reactivity in Japanese Quails (Coturnix japonica) – Narjis Kraimi, Frontiers in Physiology

Animal microbiome

Identification of circular single-stranded DNA viruses in faecal samples of Canada lynx (Lynx canadensis), moose (Alces alces) and snowshoe hare (Lepus americanus) inhabiting the Colorado San Juan Mountains – Simona Kraberger, Infection, Genetics and Evolution

Diverse novel resident Wolbachia strains in Culicine mosquitoes from Madagascar – Claire L Jeffries, bioRxiv

Sample treatment optimization for fish stool metabolomics – Takeshi Hano, Journal of Chromatography B

Plant, root, and soil microbiome

Two decades of altered snow cover does not affect soil microbial ability to catabolize carbon compounds in an oceanic alpine heath – E.R. Jasper Wubs, Soil Biology and Biochemistry

Grazing and resource availability control soil nematode body size and abundance‐mass relationship in semi‐arid grassland – W. S. Andriuzzi, Journal of Animal Ecology

Isolation and screening of antibiotic producing actinomycetes from rhizosphere and agricultural soils – Atsede Muleta, African Journal of Biotechnology

Responses of Bougainvillea spectabilis to elevated atmospheric CO2 under galaxolide (HHCB) pollution and the mechanisms of its rhizosphere metabolism – Minzhe Zhang, Journal of Soils and Sediments

Differential effect of the nitrogen form on the leaf gas exchange, amino acid composition, and antioxidant response of sweet pepper at elevated CO2 – María C. Piñero, Plant Growth Regulation

Viral metagenomics analysis and eight novel viral genomes identified from the Dushanzi mud volcanic soil in Xinjiang, China – Dan-Ting Yu, Journal of Soils and Sediments

Efficacy of Bacillus subtilis native strains for biocontrol of Phytophthora crown and root rot of pistachio in Iran – Mohammad Moradi, Tropical Plant Pathology

Modification of plant cell wall chemistry impacts metabolome and microbiome composition in Populus PdKOR1 RNAi plants – Allison M. Veach, Plant and Soil

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities – Sai Guo, European Journal of Soil Biology

Microbial communities and natural fermentation of corn silages prepared with farm bunker-silo in Southwest China – Hao Guan, Bioresource Technology

Cultivated methanotrophs associated with rhizospheres of traditional rice landraces from Western India belong to Methylocaldum and Methylocystis – Monali C. Rahalkar, 3 Biotech

Metal(loid)-resistant bacteria reduce wheat Cd and As uptake in metal(loid)-contaminated soil – Xiao-Han Wang, Environmental Pollution

Enhanced removal of nitrate in the maize rhizosphere by plant growth-promoting Bacillus megaterium NCT-2, and its colonization pattern in response to nitrate – Shaohua Chu, Chemosphere

Bioactive luteoloside produced by Myroides odoratimimus, solvent-tolerant bacterium form the rhizosphere of Lonicera japonica –  Y. X. Zhao, Natural Product Research

Potential application of selected metal resistant phosphate solubilizing bacteria isolated from the gut of earthworm (Metaphire posthuma) in plant growth promotion – Jayanta  Kumar Biswas, Geoderma

Effects of Pseudomonas chenduensis and biochar on cadmium availability and microbial community in the paddy soil – Lingjuan Li, Science of The Total Environment

Continuous application of different fertilizers induces distinct bulk and rhizosphere soil protist communities – Sai Guo, European Journal of Soil Biology

Analysis on metabolic functions of stored rice microbial communities by BIOLOG ECO microplates – Zhiwen Ge, Frontiers in Microbiology

Effects of discrete bioactive microbial volatiles on plants and fungi – Birgit Piechulla, Plant, Cell, and Environment

Phylogenetic-scale disparities in the soil microbial diversity–ecosystem functioning relationship – Marta Goberna, ISME

Similar soil microbial community structure across different environments after long‐term succession: evidence from volcanoes of different ages – Shangqi Xu, Journal of Basic Microbiology

Water and extremophile microbiome

Comparison among the microbial communities in the lake, lake wetland, and estuary sediments of a plain river network – Wei Huang, Microbiology Open

The distinctive microbial community improves composting efficiency in a full-scale hyperthermophilic composting plant – Zhen Yu, Bioresource Technology

Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom – Ivan S. Mikhailov, Microbial Ecology

The Legacy Effects of Winter Climate on Microbial Functioning After Snowmelt in a Subarctic Tundra – Maria Väisänen, Microbial Ecology

Characterization of phototrophic microorganisms and description of new cyanobacteria isolated from the saline-alkaline crater-lake Dziani Dzaha (Mayotte, Indian Ocean) – M. Cellamare, FEMS Microbiology Ecology

Methanogens in the Antarctic Dry Valley Permafrost – Tatiana A. Vishnivetskaya, FEMS Microbiology Ecology

Bacterial Diversity in an Alpine Debris-Free and Debris-Cover Accumulation Zone Glacier Ice, North Sikkim, India – Mingma Thundu Sherpa, Indian Journal of Microbiology

Culturing the ubiquitous freshwater actinobacterial acI lineage by supplying a biochemical ‘helper’ catalase – Suhyun Kim, bioRxiv

Assessing the effect of pretreatments on the structure and functionality of microbial communities for the bioconversion of microalgae to biogas – Olivia Córdova, Frontiers in Microbiology

Great Salt Lake microbiology: a historical perspective – Bonnie K. Baxter, International Microbiology

Life from the ashes: survival of dry bacterial spores after very high temperature exposure – Lynda Beladjal, Extremophiles

Microbial and geochemical controls on waste rock weathering and drainage quality – Sharon Blackmore, Science of The Total Environment

Characterization and high-throughput sequencing of a trichlorophenol-dechlorinating microbial community acclimated from sewage sludge – Jiaxiu Song, Journal of Cleaner Production

Impacts of surface-applied residues on N-cycling soil microbial communities in miscanthus and switchgrass cropping systems – Karen A. Thompson, Applied Soil Ecology

Water is a critical factor in evaluating and assessing microbial colonization and destruction of Angkor sandstone monuments – Xiaobo Liu, International Biodeterioration & Biodegradation

Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass – Justus Hardegen, Bioresource Technology

Bacterial lineages putatively associated with the dissemination of antibiotic resistance genes in a full-scale urban wastewater treatment plant – Carlos Narciso-da-Rocha, Environment International

Impact of organic waste composition on life cycle energy production, global warming and Water use for treatment by anaerobic digestion followed by composting – Sara A. Pace, Resources, Conservation and Recycling

1H NMR metabolomics of microbial metabolites in the four MW agricultural biogas plant reactors: A case study of inhibition mirroring the acute rumen acidosis symptoms – Boštjan Murovec, Journal of Environmental Management

Comparative Metagenomics Provides Insight into the Ecosystem Functioning of the Shark Bay Stromatolites, Western Australia – Joany Babilonia, Frontiers in Microbiology

Assessing the abundance of fungal populations in a full-scale membrane bioreactor (MBR) treating urban wastewater by using quantitative PCR (qPCR) – P. Maza-Márquez, Journal of Environmental Management

Food microbiology

Occurrence of lactic acid bacteria and yeasts at species and strain level during spontaneous fermentation of mawè, a cereal dough produced in West Africa – Marcel Houngbédji, Food Microbiology

Probiotics / prebiotics

Probiotics in IBD: Combining in vitro and in vivomodels for selecting strains with both anti-inflammatory potential as well as a capacity to restore the gut epithelial barrier – Mazen Zaylaa, Journal of Functional Foods

Can prebiotics assist in the management of cognition and weight gain in schizophrenia? – Amy Chia-Ching Kao, Psychoneuroendocrinology

Probiotic potentials of Lactobacillus plantarum isolated from fermented durian (Tempoyak), a Malaysian traditional condiment – Asmariah Ahmad, Food Science and Nutrition

Bioinformatics

Identifying Heritable Communities of Microbiome by Root-Unifrac and Wishart Distribution – Yunfan Tang, bioRxiv

PARTIE: a partition engine to separate metagenomic and amplicon projects in the Sequence Read Archive – Pedro J. Torres, Bioinformatics

Techniques

Dead or Alive? Molecular life-dead distinction in human stool samples reveals significantly different composition of the microbial community – Alexandra Perras, bioRxiv

Critical Assessment of Methods to Quantify Biofilm Growth and Evaluate Antibiofilm Activity of Host Defence Peptides – Evan F. Haney, Biomolecules

June 7, 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

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

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

General Microbiome

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

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

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

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

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

Gut Microbiome

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

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

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

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

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

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

Skin Microbiome

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

Oral Microbiome

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

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

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

Air and Water Microbiome

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

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

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

Animal Experiments and Microbiome

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

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

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

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

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

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

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

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

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

Plant and Soil Microbiomes

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

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

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

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

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

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

 

May 31, 2018

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

 

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