June 15, 2018

Secondary metabolite biosynthetic genes from novel soil bacteria, a human viral protein cluster metagenomic database, sleep apnea symptoms alter the gut microbiota and metabolome.

Pregnancy and early life

16S ribosomal RNA-based gut microbiome composition analysis in infants with breast milk jaundice – Miao Duan – Open Life Sciences

Human respiratory microbiome

Pre-print: New insights into human nostril microbiome from the expanded Human Oral Microbiome Database (eHOMD): a resource for species-level identification of microbiome data from the aerodigestive tract – Isabel Fernández Escapa – bioRxiv

Human oral microbiome

Review: Live and let die: hydrogen peroxide production by the commensal flora and its role in maintaining a symbiotic microbiome – Sylvio Redanz – Molecular Oral Microbiology

Human nearly-sterile sites

Cultural Isolation and Characteristics of the Blood Microbiome of Healthy Individuals – Stefan Panaiotov – Advances In Microbiology

Human gut microbiome

Sex differences in NSAID-induced perturbation of human intestinal barrier function and microbiota – Shoko Edogawa – The FASEB Journal

Animal experiments

Intermittent Hypoxia and Hypercapnia, a Hallmark of Obstructive Sleep Apnea, Alters the Gut Microbiome and Metabolome – Anupriya Tripathi – mSystems

IL-1R and MyD88 Contribute to the Absence of a Bacterial Microbiome on the Healthy Murine Cornea – Stephanie J Wan – Frontiers in Microbiology

Aflatoxin B1 Disrupts Gut-Microbial Metabolisms of Short-Chain Fatty Acids, Long-Chain Fatty Acids, and Bile Acids in Male F344 Rats – Jun Zhou – Toxicological Sciences

Metabolome and gut microbiota variation with long-term intake of Panax ginseng extracts on rats – Yifan Sun – Food & Function

Animal microbiome

Partial incubation during egg laying reduces eggshell microbial loads in a temperate‐breeding passerine – Patricia B Bollinger – Journal of Avian Biology

Bacterial and Fungal Midgut Community Dynamics and Transfer Between Mother and Brood in the Asian Longhorned Beetle (Anoplophora glabripennis), an Invasive Xylophage – Charles J Mason – Microbial Ecology

Succession of embryonic and the intestinal bacterial communities of Atlantic salmon (Salmo salar) reveals stage‐specific microbial signatures – Jep Lokesh – MicrobiologyOpen

Plant, root, and soil microbiome

Novel soil bacteria possess diverse genes for secondary metabolite biosynthesis – Alexander Crits-Christoph – Nature

Environment and host as large-scale controls of ectomycorrhizal fungi – Sietse van der Linde – Nature

Studies on Quantitative Analysis of Rhizosphere and Non-Rhizosphere Mycoflora at Different Stages of Plant Growth in Different Varieties of Pigeon Pea [Cajanus cajan (L.) Millsp.] – V Jalander – International Journal of Pure & Applied Bioscience

The Functional Potential of the Rhizospheric Microbiome of an Invasive Tree Species, Acacia dealbata – Casper N Kamutando – Microbial Ecology

Review: Plant Growth Promoting Rhizobacteria: Blessing to Agriculture – Twisha S Patel – International Journal of Pure & Applied Bioscience

Inorganic Nitrogen Application Affects Both Taxonomical and Predicted Functional Structure of Wheat Rhizosphere Bacterial Communities – Vanessa N Kavamura – Frontiers in Microbiology

Water and extremophile microbiome

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway – Gourvendu Saxena – mSystems

Phages and viruses

The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation – Ali H A Elbehery – Frontiers in Microbiology

Bioinformatics

BioSankey: Visualization of Microbial Communities Over Time – Alexander Platzer – Journal of Integrative Bioinformatics

Pre-print: Understanding trivial challenges of microbial genomics: An assembly example – Delphine Lariviere – bioRxiv

Microbes in the news

Faecal transplants could help preserve vulnerable species – Sara Reardon – Nature

Science, career, and publishing

Pre-print: Researchers preferentially collaborate with same-gendered colleagues across the life sciences – Luke Holman – bioRxiv

Pre-print: Attitudes, Perceptions and Barriers to Research and Publishing among Research and Teaching Staff: A Case Study – Stanley Irobekhian Reuben Okoduwa – 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 12, 2018

Gut and General Microbiome

Screening for Nonalcoholic Fatty Liver Disease in Inflammatory Bowel Diseases: A Cohort Study Using Transient Elastography – Chiara Saroli Palumbo – Inflammatory Bowel Diseases

Review: A critical appraisal of advances in the diagnosis of diverticular disease – Antonio Tursi – Expert Review of Gastroenterology & Hepatology  

Antimicrobial-Induced Cytopenia and Bone Marrow Hypocellularity in Patients with Cirrhosis – Anupama Patil – Bone Marrow Research

Colonic Mucosal Microbiota in Colorectal Cancer: A Single-Center Metagenomic Study in Saudi Arabia – Ahmed O. Alomair – Gastroenterology Research and Practice

Connecting homocysteine and obesity through pyroptosis, gut microbiome, epigenetics, peroxisome proliferator-activator receptor γ (PPARγ) and zinc finger protein 407 (Zfp407) – Anwesha Laha – Canadian Journal of Physiology and Pharmacology

Review: Sexual dimorphism of cardiometabolic dysfunction: Gut microbiome in the play? – Tzu-Wen L. Cross – Molecular Metabolism

Individuality and convergence of the infant gut microbiota during the first year of life – Eric J. de Muinck – Nature Communications

Reconstruction of the bifidobacterial pan-secretome reveals the network of extracellular interactions between bifidobacteria and the infant gutGabriele Andrea Lugli – Applied and Environmental Microbiology

Commentary: Beyond Oxalobacter: the gut microbiota and kidney stone formation – Gwen Falony – Gut

Nutritional modulation of the intestinal microbiota: future opportunities for the prevention and treatment of neuroimmune and neuroinflammatory disease – Vincent C.Lombardi – The Journal of Nutritional Biochemistry

 

Reproductive and Urinary Tract Microbiome

Review: Implantation failure of endometrial origin: what is new? –  Jose Bellver – Current Opinion in Obstetrics and Gynecology

Detecting viral genomes in the female urinary microbiome – Andrea Garretto – Journal of General Virology

Commentary: Regional Caesarean Delivery Practices, the Maternal-Infant Microbiome, and Risk for Asthma – Rebecca Entz – Journal of Obstetrics and Gynaecology Canada

 

Skin Microbiome

Insights into the skin microbiome dynamics of leprosy patients during multi-drug therapy and in healthy individuals from Brazil – Paulo E. S. Silva – Scientific Reports

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

 

Oral and Respiratory Microbiome

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

Bacterial biogeography of adult airways in atopic asthma – Juliana Durack – Microbiome

Review: Adenotonsillar microbiome: an update – James Jordan Johnston – Postgraduate Medical Journal

 

Animal Microbiome

The canine gut microbiome is associated with higher risk of gastric dilatation-volvulus and high risk genetic variants of the immune system – Meredith A. J. Hullar – PLOS ONE

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 & Food Research

Deficiency of BrpA in Streptococcus mutans Reduces Virulence in Rat Caries Model – Zezhang T. Wen – Molecular Oral Microbiology

Huddling remodels gut microbiota to reduce energy requirements in a small mammal species during cold exposure – Xue-Ying Zhang – Microbiome

Abnormal gut microbiota composition contributes to cognitive dysfunction in SAMP8 mice – Gaofeng Zhan – Aging

The role of regulator FucP in Edwardsiella tarda pathogenesis and the inflammatory cytokine response in tilapia – Jiayan Wu – Fish & Shellfish Immunology

Malassezia pachydermatis from animals: Planktonic and biofilm antifungal susceptibility and its virulence arsenal – Raimunda Sâmia Nogueira Brilhante – Veterinary Microbiology

 

Beneficial Microbes

Oral administration of Bifidobacterium bifidum TMC3115 to neonatal mice may alleviate IgE-mediated allergic risk in adulthood – R.Y. Cheng – Beneficial Microbes

Three-Month Feeding Integration With Bifidobacterium Strains Prevents Gastrointestinal Symptoms in Healthy Newborns – Irene Aloisio – Frontiers in Nutrition

 

Bioinformatics and Genomics

Review: Interrogating the microbiome: experimental and computational considerations in support of study reproducibility – Carine Poussin – Drug Discovery Today

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software – Toby J. Wilkinson – Frontiers in Microbiology

Benchmark Evaluation of True Single Molecular Sequencing to Determine Cystic Fibrosis Airway Microbiome Diversity – Andrea Hahn – Frontiers in Microbiology

Next-Generation Machine Learning for Biological Networks – Diogo M. Camacho – Cell

 

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 27, 2018

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

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