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 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

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 9, 2018

Human respiratory microbiome

Lung Dysbiosis, Inflammation, and Injury in Hematopoietic Cell Transplantation – David N O’Dwyer, American Journal of Respiratory and Critical Care Medicine

Heterogeneity of Microbiota Dysbiosis in Chronic Rhinosinusitis: Potential Clinical Implications and Microbial Community Mechanisms Contributing to Sinonasal Inflammation – Keehoon Lee, Frontiers in Cell and Infection Microbiology

Human skin microbiome

A systematic literature review of the human skin microbiome as biomarker for dermatological drug development – T. van der Kolk, British Journal of Clinical Pharmacology

Human gut microbiome

Inadequate Vitamin C Status in Prediabetes and Type 2 Diabetes Mellitus: Associations with Glycaemic Control, Obesity, and Smoking – Renée Wilson, Nutrients

Altered Stool Microbiota of Infants with Cystic Fibrosis Shows Reduction in Genera Associated with Immune Programming – Katherine Anosca, bioRxiv

Gut Microbiota Diversity across Ethnicities in the United States – Andrew W Brooks, bioRxiv

From the Mediterranean Diet to the Microbiome – Caroline E Childs, The Journal of Nutrition

Letter: improvements in mental health after faecal microbiota transplantation—an underexplored treatment‐related benefit? – B. H. Mullish, Alimentary Pharmacology and Therapeutics

Letter: improvements in mental health after faecal microbiota transplantation—an underexplored treatment‐related benefit? Authors’ reply – J. Jalanka, Alimentary Pharmacology and Therapeutics

Microbiota‐gut‐brain axis: Interaction of gut microbes and their metabolites with host epithelial barriers – Y. Bhattarai, Neurogastroenterology & Motility

Animal experiments

Bisphenol-A alters microbiota metabolites derived from aromatic amino acids and worsens disease activity during colitis – Jennifer AA DeLuca, Experimental Biology and Medicine

Fumonisin-Exposure Impairs Age-Related Ecological Succession of Bacterial Species in Weaned Pig Gut Microbiota – Ivan Mateos, Toxins

Ethanol extract of Ganoderma lucidum ameliorates lipid metabolic disorders and modulates the gut microbiota composition in high-fat diet fed rats – Wei-Ling Guo, Food & Function

Gut microbiota promotes production of aromatic metabolites through degradation of barley leaf fiber – Daotong Li, The Journal of Nutritional Biochemistry

Dietary Supplementation of Potato Peel Powders Prepared from Conventional and Organic Russet and Non-organic Gold and Red Potatoes Reduces Weight Gain in Mice on a High-Fat Diet – Salem Elkahoui, Journal of Agricultural and Food Chemistry

Microbial dysbiosis associated with impaired intestinal Na+/H+ exchange accelerates and exacerbates colitis in ex-germ free mice – Christy A. Harrison, Mucosal Immunology

Animal microbiome

Comparison of Channel Catfish and Blue Catfish Gut Microbiota Assemblages Shows Minimal Effects of Host Genetics on Microbial Structure and Inferred Function – Jacob W. Bledsoe, Frontiers in Microbiology

Inter-individual variability in copepod microbiomes reveals bacterial networks linked to host physiology – Manoshi S. Datta, The ISME Journal

Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds – Jessy Vibin, Scientific Reports

Microorganism’s adaptation of Crucian carp may closely relate to its living environments – Huanxin Zhang, Microbiology Open

Diversity, specificity, co-occurrence and hub taxa of the bacterial–fungal pollen microbiome – Binoy Ambika Manirajan, FEMS Microbiology Ecology

Differential carbohydrate utilization and organic acid production by honey bee symbionts – Fredrick J Lee, FEMS Microbiology Ecology

Plant, root, and soil microbiome

The effect of periphyton on seed germination and seedling growth of rice (Oryza sativa) in paddy area – Haiying Lu, Science of The Total Environment

Diversity of Bacteria and the Characteristics of Actinobacteria Community Structure in Badain Jaran Desert and Tengger Desert of China – Ye Sun, Frontiers in Microbiology

Vancomycin and/or Multidrug-Resistant Citrobacter Freundii Altered the Metabolic Pattern of Soil Microbial Community – Mariusz Cycoń, Frontiers in Microbiology

Degradation of dibutyl phthalate in two contrasting agricultural soils and its long-term effects on soil microbial community – Jinjin Cheng, Science of The Total Environment

Impact of Bactrocera oleae on the fungal microbiota of ripe olive drupes – Ahmed Abdelfattah, bioRxiv

Potential of Finger Millet Indigenous Rhizobacterium Pseudomonas sp. MSSRFD41 in Blast Disease Management—Growth Promotion and Compatibility With the Resident Rhizomicrobiome – Jegan Sekar, Frontiers in Microbiology

Biochars from olive mill waste have contrasting effects on plants, fungi and phytoparasitic nematodes – Roberta Marra, Plos One

Water and extremophile microbiome 

Effects of Ice-Algal Aggregate Export on the Connectivity of Bacterial Communities in the Central Arctic Ocean – Josephine Z. Rapp, Frontiers in Microbiology

Built environment

The Airplane Cabin Microbiome – Howard Weiss, Microbial Ecology

Food microbiology

Sequencing of the Cheese Microbiome and Its Relevance to Industry – Bhagya. R. Yeluri Jonnala, Frontiers in Microbiology

Comparison of Bacterial Diversity Between Two Traditional Starters and the Round-Koji-Maker Starter for Traditional Cantonese Chi-Flavor Liquor Brewing – Jie Wang, Frontiers in Microbiology

Microbial ecology

Syntrophic growth with direct interspecies electron transfer between pili-free Geobacter species – Xing Liu, The ISME Journal

Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics – Amanda N Shelton, bioRxiv

Microbial Diversity and Nitrogen‐metabolizing Gene Abundance in Backyard Food Waste Composting Systems – T. C. Weglarz, Journal of Applied Microbiology

Enhancement of methanogenesis by electric syntrophy with biogenic iron‐sulfide minerals – Souichiro Kato, Microbiology Open

Probiotics/Prebiotics

Probiotics Ameliorate Stool Consistency in Patients with Chronic Constipation: A Randomized, Double-Blind, Placebo-Controlled Study – Jin Young Yoon, Digestive Diseases and Sciences

Supplementation of p40, a Lactobacillus rhamnosus GG-derived protein, in early life promotes epidermal growth factor receptor-dependent intestinal development and long-term health outcomes – Xi Shen, Mucosal Immunology

Bioinformatics

Detection of Multidimensional Co-Exclusion Patterns in Microbial Communities – Levent Albayrak, Bioinformatics

 

June 6, 2018

 

Today’s highlights: Microbes on aging flue-cured tobaccos, impact of gut microbes on neurological disease, gut microbiome of non-human microbiome, diet simplification selects for high gut microbial diversity.

General microbiome

Species Diversity and Functional Prediction of Surface Bacterial Communities on Aging Flue-Cured Tobaccos – F Wang – Current Microbiology

Oxygen restriction induces a viable but non-culturable population in bacteria – LA Kvich – bioRxiv

Human respiratory microbiome

Airway Microbiota Is Associated with Up-Regulation of the PI3K Pathway in Lung Cancer – J-C J Tsay – American Journal of Respiratory and Critical Care Medicine

Human skin microbiome

Role of anaerobes in polymicrobial communities and biofilms complicating diabetic foot ulcers – SL Percival – International Wound Journal

Human gut microbiome

Impact of gut microbiota on neurological diseases: Diet composition and novel treatments – A L-Garcia – Critical Reviews in Food Science and Nutrition

Composition and richness of the serum microbiome differ by age and link to systemic inflammation – TW Buford – GeroScience

Animal microbiome 

Review: The gut microbiome of nonhuman primates: Lessons in ecology and evolution – JB Clayton – American Journal of Primatology

Culture-based analysis of Pristionchus-associated microbiota from beetles and figs for studying nematode-bacterial interactions – N Akduman – PLoS One

Diet simplification selects for high gut microbial diversity and strong fermenting ability in high-altitude pikas – H Li – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Rhizospheric bacterial isolates of grass pea (Lathyrus sativus L.) endowed with multiple plant growth promoting traits – A Mussa – Journal of Applied Microbiology

Diversity of culturable methylotrophic bacteria in different genotypes of groundnut and their potential for plant growth promotion – R. Krishnamoorthy – 3 Biotech

Environmental factors shaping the diversity of bacterial communities that promote rice production – Z Wu – BMC Microbiology

Water and extremophile microbiome 

Basin-scale seasonal changes in marine free-living bacterioplankton community in the Ofunato Bay – MS Reza – Gene

Decay of sewage-associated bacterial communities in fresh and marine environmental waters and sediment – W Ahmed – Applied Microbiology and Biotechnology

 

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.